X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 50 mM MOPS pH 7, 50-200 mM AMMONIUM SULFATE, 50 mM MnCl2, 6-9% PEG-3350 , VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.2 α = 90
b = 153.83 β = 90
c = 52.4 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm Multilayer mirror, curved to focus in the vertical (R = 400 m) 2010-03-26
Diffraction Radiation
Monochromator Protocol
Bent Si (111) crystal, horizontally focusing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-2 1.03796 MAX II I911-2

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.75 30 99.9 0.069 -- -- 5.6 64706 64658 -- -3.0 26.278
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.75 1.8 100.0 0.619 -- 3.06 6.0 4688

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.75 29.021 -- 2.0 -- 64592 2586 99.96 -- 0.1582 0.1571 0.1843 Random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.75 1.7837 3513 141 3372 0.2315 0.2597 -- 100.0
X Ray Diffraction 1.7837 1.8201 3554 142 3412 0.2121 0.2466 -- 100.0
X Ray Diffraction 1.8201 1.8596 3528 141 3387 0.1942 0.2358 -- 100.0
X Ray Diffraction 1.8596 1.9029 3531 141 3390 0.1794 0.1926 -- 100.0
X Ray Diffraction 1.9029 1.9505 3552 143 3409 0.162 0.1752 -- 100.0
X Ray Diffraction 1.9505 2.0032 3558 142 3416 0.1521 0.197 -- 100.0
X Ray Diffraction 2.0032 2.0621 3539 142 3397 0.1507 0.1791 -- 100.0
X Ray Diffraction 2.0621 2.1287 3552 142 3410 0.1518 0.1865 -- 100.0
X Ray Diffraction 2.1287 2.2047 3566 143 3423 0.1498 0.1799 -- 100.0
X Ray Diffraction 2.2047 2.293 3593 143 3450 0.1436 0.183 -- 100.0
X Ray Diffraction 2.293 2.3973 3554 143 3411 0.1508 0.18 -- 100.0
X Ray Diffraction 2.3973 2.5236 3575 143 3432 0.1552 0.2018 -- 100.0
X Ray Diffraction 2.5236 2.6816 3587 143 3444 0.1513 0.2055 -- 100.0
X Ray Diffraction 2.6816 2.8885 3616 145 3471 0.163 0.2059 -- 100.0
X Ray Diffraction 2.8885 3.1788 3598 144 3454 0.1557 0.1846 -- 100.0
X Ray Diffraction 3.1788 3.6381 3649 146 3503 0.1479 0.152 -- 100.0
X Ray Diffraction 3.6381 4.5807 3680 148 3532 0.1316 0.1561 -- 100.0
X Ray Diffraction 4.5807 29.025 3847 154 3693 0.1755 0.1853 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic+tls
Mean Isotropic B 22.1828
Anisotropic B[1][1] 5.207
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.2905
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.9166
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.415
f_plane_restr 0.007
f_chiral_restr 0.089
f_angle_d 1.246
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4720
Nucleic Acid Atoms 0
Heterogen Atoms 139
Solvent Atoms 546

Software

Computing
Computing Package Purpose
MARCCD Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser version: 2.1.4 molecular replacement
Xscale data reduction