Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints.
Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints.
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在 1.0 A 条件下（有限制和无限制）对来自脱硫弧菌的红氧还蛋白进行精制。
DOI：
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发表时间：
1992
期刊：
影响因子：
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通讯作者：
K. Wilson
中科院分区：
文献类型：
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作者：
Z. Dauter;L. Sieker;K. Wilson
利用同步辐射和密封管Mo K α源的x射线，记录了从普通脱硫弧菌中提取的红霉素晶体的x射线数据，分辨率为1.0 a。在这两种情况下，成像板扫描仪被用作探测器。晶体的空间群为P2(1)，胞元尺寸a = 19.97, b = 41.45, c = 24.41 a, β = 108.3度。对称相关反射之间的总体合并R(I)因子为5.8%。在立体化学约束下，采用最小二乘最小化法对模型进行了优化，R因子为16.4%。只使用了原子位置参数和各向同性温度因子对非氢原子进行了细化。有18532个独立的x射线观测，总共有1916个原子参数。一轮无限制的改进得到了16.0%的R因子，90%以上的蛋白质原子的几何形状是可以接受的，但强调了8个残基固有的无序性。最后一轮的约束细化给出了14.7%的R因子。分子中389个蛋白质原子中的3个位于Lys2的侧链上，在模型中被分配为零占用。三个侧链上共有8个原子被分配了两种构象，在模型中有393个蛋白质原子位点。此外还有一个铁原子，一个硫酸盐离子和102个水点。339个氢原子被包括在它们的计算位置上，它们没有被精炼。有明确的证据表明存在各向异性热运动。这一点尚未纳入目前的模式。
X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha source. In both cases an imaging-plate scanner was used as detector. The space group of the crystals is P2(1) with cell dimensions a = 19.97, b = 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in the refinement. There were 18,532 independent X-ray observations for a total of 1916 atomic parameters. A round of unrestrained refinement gave an R factor of 16.0%, acceptable geometry for more than 90% of the protein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model.