X-RAY CRYSTALLOGRAPHY OF MACROMOLECULES

大分子的 X 射线晶体学

• 批准号: 2701703
• 负责人: ZBYSZEK OTWINOWSKI
• 金额: $ 30.52万
• 依托单位: UT SOUTHWESTERN MEDICAL CENTER
• 依托单位国家: 美国
• 财政年份: 1996
• 资助国家: 美国
• 起止时间: 1996-05-01 至 1999-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2701703
• 关键词: X ray crystallography; computer program /software; computer simulation; computer system design /evaluation; mathematics; method development; statistics /biometry; structural biology

This proposal is in response to the recent, dramatic expansion in the fields of structural biology. Progress in genetics and biochemistry created a need for precise stereochemical understanding of large numbers of macromolecules. Progress in X-ray instrumentation and computing hardware makes this possible. Based on our experience in developing the widely used macromolecular X-ray crystallography HKL data reduction package (Denzo, Scalepack, XdisplayF) we propose to further develop this area. The specific aims of this proposal are: 1) to develop data reduction methods for imperfect crystals - highly mosaic or twinned. it will be possible to index more than one diffraction pattern in one detector image, calculate overlap between diffraction patterns and correct for Bragg peak tails of reflection intruding upon each other. 2) to expand the Multiwavelength Anomalous Dispersion (MAD) method to cases where the signal-to-error ratio is currently insufficient for structure determination. This will be accomplished by calibrating and correcting for instrument response factors that now limit the MAD method to well diffracting crystals with relatively high anomalous diffraction signal. 3) to provide optimal data collection strategy by simulating in advance of data collection the expected reciprocal space coverage and detector resolution as a function of possible settings - data collection angles and crystal-to-detector distance. 4) to provide real-time feedback by reducing data on-line and calculating synthetic statistics. This is of particular significance to users of synchrotron facilities who need to wait for months to repeat their experiments. 5) to expand the range of the crystallographic experiments treated optimally in data reduction by deconvolution of partially overlapping reflections and 3-D profile fitting, to develop automatic and interactive editing tools in order to minimize the influence of possible experimental artifacts on the reduced data. 6) to expand methods to visually inspect the process of data collection and data reduction from current direct visualization of raw data to synthetic visual representation of factors affecting data quality - average reflection profiles, de convolution integrals, crystal slippage, detector response function and others. 7) to provide data base style organizational tools for the experimenter to follow the entire crystallographic project. The data base will be used to create unified reports - merging statistics, coverage, decay, slippage etc. Lastly, all of the above developments will be integrated into one efficient, simple to use computer and detector general software package. The resulting software will increase precision and reliability of three-D structures of macromolecules by x-ray crystallography, enable to solve crystal structures too difficult to solve with the present methods, and will speed-up, simplify and reduce the time and effort required of the structure determination process, speeding up understanding of biological systems and structure based drug design.

该提案是为了应对最近的急剧扩张 结构生物学领域。 遗传学和生物化学进展 产生了对大量的精确立体化学理解的需要 大分子。 X 射线仪器和计算硬件的进展 使这成为可能。 基于我们开发广泛使用的 大分子X射线晶体学HKL数据缩减包（Denzo， Scalepack、XdisplayF）我们建议进一步开发这一领域。 这 该提案的具体目标是： 1）开发不完美晶体的数据缩减方法——高度 马赛克或孪生。 将有可能索引多个衍射 一张探测器图像中的图案，计算衍射之间的重叠 模式并纠正侵入反射的布拉格峰尾 彼此。 2）将多波长反常色散（MAD）方法扩展到 目前信差比不足以满足的情况 结构测定。 这将通过校准和 校正仪器响应因素，这些因素现在将 MAD 方法限制为 具有相对较高反常衍射的良好衍射晶体 信号。 3）通过预先模拟提供最优的数据采集策略 数据收集 预期的倒数空间覆盖范围和探测器 分辨率作为可能设置的函数 - 数据收集角度和 晶体到探测器的距离。 4）通过减少在线数据和计算来提供实时反馈 综合统计。 这对用户来说尤其重要 同步加速器设施需要等待数月才能重复 实验。 5）扩大晶体学实验处理的范围 通过部分重叠的反卷积优化数据缩减 反射和 3D 轮廓拟合，开发自动和交互式 编辑工具，以尽量减少可能的实验的影响 减少数据上的伪影。 6）扩展目视检查数据收集过程的方法 并将数据从当前原始数据的直接可视化减少到 影响数据质量因素的综合视觉表示 - 平均 反射剖面、反卷积积分、晶体滑移、探测器 响应函数等。 7）为实验者提供数据库式的组织工具 跟踪整个晶体学项目。 该数据库将用于 创建统一的报告 - 合并统计数据、覆盖范围、衰减、滑点等。 最后，所有上述发展将被整合到一个 高效、简单易用的计算机和检测器通用软件包。 由此产生的软件将提高三维的精度和可靠性 通过 X 射线晶体学分析大分子结构，能够解决 晶体结构很难用现有方法解决，并且 将加速、简化并减少所需的时间和精力 结构测定过程，加速对生物的理解 基于系统和结构的药物设计。