X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 289.0
Details 100mM sodium acetate, 2.9-3.3M sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.23 α = 90
b = 121.97 β = 90
c = 405.21 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-02-18
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U

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
2.9 50 84.2 0.172 -- -- 5.3 -- 99156 -- -- --
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)
2.9 3.0 86.8 -- -- -- 4.7 10058

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
FOURIER SYNTHESIS 3.002 44.714 -- 1.34 -- 88840 1585 82.97 -- 0.245 0.2446 0.2708 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 3.0021 3.099 -- 134 7663 0.3841 0.3838 -- 81.0
X Ray Diffraction 3.099 3.2097 -- 151 8094 0.3619 0.4089 -- 86.0
X Ray Diffraction 3.2097 3.3382 -- 146 8085 0.3301 0.314 -- 86.0
X Ray Diffraction 3.3382 3.49 -- 153 8032 0.2805 0.2913 -- 85.0
X Ray Diffraction 3.49 3.674 -- 147 8048 0.2668 0.3001 -- 85.0
X Ray Diffraction 3.674 3.904 -- 138 7993 0.2416 0.2806 -- 84.0
X Ray Diffraction 3.904 4.2053 -- 133 8012 0.2228 0.2283 -- 84.0
X Ray Diffraction 4.2053 4.6281 -- 151 7902 0.1997 0.2507 -- 83.0
X Ray Diffraction 4.6281 5.2968 -- 144 7864 0.204 0.2258 -- 82.0
X Ray Diffraction 5.2968 6.6699 -- 142 7840 0.2235 0.246 -- 81.0
X Ray Diffraction 6.6699 44.719 -- 146 7722 0.226 0.2576 -- 77.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 82.4269
Anisotropic B[1][1] 18.8473
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.8306
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -21.6778
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.81
f_plane_restr 0.001
f_chiral_restr 0.03
f_angle_d 0.421
f_bond_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22127
Nucleic Acid Atoms 0
Heterogen Atoms 147
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction