X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.4
Temperature 293.0
Details 0.01 M sodium acetate, 25% saturated ammonium sulfate, 0.1 M glycin/HCl buffer, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.06 α = 90
b = 107.06 β = 90
c = 311.2 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2011-10-23
Diffraction Radiation
Monochromator Protocol
horizontally focusing Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13

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
1.94 29.5 98.2 0.172 -- -- -- 78881 77457 0.0 -3.0 --

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 1.94 7.998 -- 1.99 77457 76180 3809 98.25 -- 0.1827 0.1803 0.2256 --
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 1.94 1.9642 -- 126 2395 0.438 0.478 -- 90.0
X Ray Diffraction 1.9642 1.9897 -- 140 2673 0.3422 0.3657 -- 98.0
X Ray Diffraction 1.9897 2.0165 -- 139 2641 0.3112 0.3608 -- 98.0
X Ray Diffraction 2.0165 2.0448 -- 137 2585 0.2996 0.3691 -- 98.0
X Ray Diffraction 2.0448 2.0748 -- 138 2624 0.2796 0.3235 -- 97.0
X Ray Diffraction 2.0748 2.1067 -- 137 2613 0.2522 0.2736 -- 97.0
X Ray Diffraction 2.1067 2.1406 -- 138 2624 0.2372 0.2985 -- 97.0
X Ray Diffraction 2.1406 2.1768 -- 138 2607 0.2527 0.3219 -- 97.0
X Ray Diffraction 2.1768 2.2155 -- 136 2598 0.2705 0.3492 -- 97.0
X Ray Diffraction 2.2155 2.2572 -- 138 2606 0.2701 0.3935 -- 97.0
X Ray Diffraction 2.2572 2.3022 -- 139 2647 0.2602 0.3117 -- 98.0
X Ray Diffraction 2.3022 2.351 -- 141 2680 0.2241 0.3194 -- 98.0
X Ray Diffraction 2.351 2.4043 -- 140 2658 0.1961 0.2621 -- 99.0
X Ray Diffraction 2.4043 2.4627 -- 140 2667 0.1713 0.2543 -- 99.0
X Ray Diffraction 2.4627 2.5272 -- 141 2667 0.1783 0.2314 -- 98.0
X Ray Diffraction 2.5272 2.5991 -- 140 2662 0.1796 0.2253 -- 98.0
X Ray Diffraction 2.5991 2.6799 -- 142 2695 0.1963 0.2827 -- 98.0
X Ray Diffraction 2.6799 2.7719 -- 141 2689 0.1898 0.2126 -- 100.0
X Ray Diffraction 2.7719 2.8779 -- 144 2729 0.1671 0.249 -- 100.0
X Ray Diffraction 2.8779 3.0022 -- 144 2741 0.1608 0.2055 -- 100.0
X Ray Diffraction 3.0022 3.1513 -- 145 2754 0.1586 0.2372 -- 100.0
X Ray Diffraction 3.1513 3.3352 -- 144 2739 0.1762 0.2107 -- 100.0
X Ray Diffraction 3.3352 3.5713 -- 147 2780 0.1632 0.2183 -- 100.0
X Ray Diffraction 3.5713 3.8926 -- 145 2756 0.147 0.1876 -- 100.0
X Ray Diffraction 3.8926 4.3734 -- 147 2788 0.122 0.1532 -- 100.0
X Ray Diffraction 4.3734 5.2389 -- 149 2832 0.1303 0.1476 -- 99.0
X Ray Diffraction 5.2389 7.9976 -- 153 2921 0.1946 0.2306 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.019
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.019
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.0381
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.071
f_dihedral_angle_d 13.344
f_angle_d 1.011
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3916
Nucleic Acid Atoms 0
Heterogen Atoms 177
Solvent Atoms 231

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser molecular replacement
Xscale data reduction
DENZO data collection