X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.1
Temperature 277.0
Details 7.2% isopropanol, 50 mM citrate buffer, pH 4.1, 0.1 M potassium thiocyanate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.83 α = 90
b = 74.63 β = 90
c = 76.47 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 ADSC QUANTUM 315 -- 2012-05-03
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 0.979 ALS 8.2.2

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
1.7 50 96.3 0.06 -- -- 6.5 36581 35213 0.0 0.0 --
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)
1.695 1.76 77.4 0.316 -- -- 4.0 2760

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 1.695 45.612 -- 0.0 36828 35168 1757 95.5 0.1777 0.1777 0.176 0.2068 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 1.695 1.7408 -- 77 1806 0.2623 0.3202 -- 68.0
X Ray Diffraction 1.7408 1.792 -- 127 2213 0.2155 0.2654 -- 84.0
X Ray Diffraction 1.792 1.8499 -- 139 2412 0.2032 0.2665 -- 92.0
X Ray Diffraction 1.8499 1.916 -- 127 2626 0.2027 0.268 -- 98.0
X Ray Diffraction 1.916 1.9927 -- 132 2656 0.1786 0.2651 -- 100.0
X Ray Diffraction 1.9927 2.0834 -- 139 2671 0.1761 0.2197 -- 100.0
X Ray Diffraction 2.0834 2.1933 -- 125 2684 0.1716 0.2157 -- 100.0
X Ray Diffraction 2.1933 2.3307 -- 139 2682 0.1723 0.2139 -- 100.0
X Ray Diffraction 2.3307 2.5106 -- 136 2670 0.1785 0.2281 -- 100.0
X Ray Diffraction 2.5106 2.7632 -- 142 2704 0.1912 0.2239 -- 100.0
X Ray Diffraction 2.7632 3.163 -- 147 2708 0.1813 0.1953 -- 100.0
X Ray Diffraction 3.163 3.9847 -- 149 2738 0.1605 0.2018 -- 100.0
X Ray Diffraction 3.9847 45.6287 -- 178 2841 0.1665 0.1728 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.5885
Anisotropic B[1][1] -8.1523
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.041
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.1113
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.313
f_plane_restr 0.004
f_chiral_restr 0.069
f_angle_d 1.005
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2297
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 257

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction