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 = 106.64 α = 90
b = 122.53 β = 90
c = 403.48 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 -- 2012-02-17
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.979305 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
3.19 50 99.5 0.175 -- -- 7.3 88841 88841 -- -- --
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)
3.2 3.31 99.4 0.557 -- -- 7.5 8740

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 3.187 48.796 -- 1.34 -- 88617 1592 99.27 -- 0.2361 0.2355 0.2697 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 3.187 3.2899 -- 141 7678 0.316 0.3604 -- 98.0
X Ray Diffraction 3.2899 3.4074 -- 146 7811 0.285 0.3087 -- 99.0
X Ray Diffraction 3.4074 3.5438 -- 132 7827 0.2718 0.3203 -- 99.0
X Ray Diffraction 3.5438 3.7051 -- 148 7858 0.2557 0.3062 -- 99.0
X Ray Diffraction 3.7051 3.9003 -- 143 7858 0.2411 0.2977 -- 100.0
X Ray Diffraction 3.9003 4.1446 -- 141 7871 0.2246 0.249 -- 100.0
X Ray Diffraction 4.1446 4.4644 -- 149 7884 0.2111 0.2312 -- 100.0
X Ray Diffraction 4.4644 4.9133 -- 147 7960 0.1977 0.2035 -- 100.0
X Ray Diffraction 4.9133 5.6233 -- 145 7983 0.2227 0.2636 -- 100.0
X Ray Diffraction 5.6233 7.0813 -- 144 8055 0.2259 0.264 -- 100.0
X Ray Diffraction 7.0813 48.8021 -- 156 8240 0.241 0.2817 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 84.4398
Anisotropic B[1][1] 26.0357
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.5667
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -26.6024
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 9.734
f_plane_restr 0.002
f_chiral_restr 0.035
f_angle_d 0.532
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22127
Nucleic Acid Atoms 0
Heterogen Atoms 84
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