X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 291.0
Details 13% PEG 3350, 9% iso-propanol, 0.1M Tris pH 9.0, vapor diffusion, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.47 α = 90
b = 98.63 β = 110.96
c = 73.21 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-06-19
Diffraction Radiation
Monochromator Protocol
Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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 50 98.0 0.055 -- -- -- 91609 91609 0.0 -3.0 31.826
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 85.3 0.422 -- 1.96 -- --

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 1.754 32.926 -- 1.99 91605 91605 4581 98.08 -- 0.172 0.1705 0.2019 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 1.754 1.7741 -- 116 2206 0.2751 0.3005 -- 75.0
X Ray Diffraction 1.7741 1.7949 -- 144 2734 0.2405 0.2582 -- 93.0
X Ray Diffraction 1.7949 1.8168 -- 148 2819 0.2245 0.3084 -- 96.0
X Ray Diffraction 1.8168 1.8398 -- 155 2934 0.2098 0.2657 -- 99.0
X Ray Diffraction 1.8398 1.864 -- 155 2956 0.1881 0.2101 -- 100.0
X Ray Diffraction 1.864 1.8896 -- 155 2941 0.1855 0.2457 -- 100.0
X Ray Diffraction 1.8896 1.9166 -- 155 2945 0.1818 0.2065 -- 100.0
X Ray Diffraction 1.9166 1.9452 -- 154 2921 0.1811 0.2163 -- 100.0
X Ray Diffraction 1.9452 1.9756 -- 156 2967 0.1745 0.2219 -- 100.0
X Ray Diffraction 1.9756 2.0079 -- 154 2913 0.1773 0.2154 -- 100.0
X Ray Diffraction 2.0079 2.0426 -- 155 2946 0.1668 0.2099 -- 100.0
X Ray Diffraction 2.0426 2.0797 -- 156 2967 0.1669 0.2063 -- 100.0
X Ray Diffraction 2.0797 2.1197 -- 154 2934 0.1636 0.1943 -- 100.0
X Ray Diffraction 2.1197 2.1629 -- 155 2937 0.1633 0.2237 -- 100.0
X Ray Diffraction 2.1629 2.21 -- 156 2960 0.1587 0.1931 -- 100.0
X Ray Diffraction 2.21 2.2614 -- 154 2928 0.159 0.1945 -- 100.0
X Ray Diffraction 2.2614 2.3179 -- 154 2925 0.1589 0.1911 -- 100.0
X Ray Diffraction 2.3179 2.3806 -- 155 2961 0.1585 0.2047 -- 100.0
X Ray Diffraction 2.3806 2.4506 -- 156 2949 0.1623 0.2074 -- 100.0
X Ray Diffraction 2.4506 2.5297 -- 155 2956 0.1628 0.2129 -- 100.0
X Ray Diffraction 2.5297 2.62 -- 155 2935 0.1641 0.1992 -- 99.0
X Ray Diffraction 2.62 2.7249 -- 154 2926 0.1749 0.196 -- 99.0
X Ray Diffraction 2.7249 2.8488 -- 154 2928 0.1749 0.196 -- 99.0
X Ray Diffraction 2.8488 2.9989 -- 153 2914 0.1832 0.2188 -- 99.0
X Ray Diffraction 2.9989 3.1867 -- 156 2968 0.1739 0.2143 -- 99.0
X Ray Diffraction 3.1867 3.4325 -- 154 2911 0.18 0.1847 -- 99.0
X Ray Diffraction 3.4325 3.7775 -- 154 2938 0.1669 0.2101 -- 99.0
X Ray Diffraction 3.7775 4.323 -- 154 2927 0.15 0.1735 -- 98.0
X Ray Diffraction 4.323 5.4426 -- 155 2946 0.1542 0.1654 -- 98.0
X Ray Diffraction 5.4426 32.926 -- 150 2832 0.1834 0.2125 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.8155
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.455
f_plane_restr 0.006
f_chiral_restr 0.083
f_angle_d 1.184
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6433
Nucleic Acid Atoms 234
Heterogen Atoms 0
Solvent Atoms 470

Software

Computing
Computing Package Purpose
CBASS Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
Xscale data reduction