X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 3.5M Sodium Formate, pH 7.0, vapor diffusion, hanging drop, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.88 α = 90
b = 95.18 β = 90
c = 117.02 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 -- 2010-07-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E

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
2.65 29.44 97.1 0.142 -- -- -- -- 14792 -- -3.0 30.581
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)
2.65 2.72 99.1 0.481 -- 3.47 -- --

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 2.65 29.441 -- 2.01 -- 14754 738 97.24 -- 0.2247 0.2221 0.2728 --
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 2.65 2.8545 -- 148 2793 0.2821 0.3247 -- 99.0
X Ray Diffraction 2.8545 3.1414 -- 146 2788 0.262 0.3101 -- 99.0
X Ray Diffraction 3.1414 3.5953 -- 147 2787 0.2337 0.3169 -- 98.0
X Ray Diffraction 3.5953 4.5271 -- 148 2802 0.1957 0.241 -- 97.0
X Ray Diffraction 4.5271 29.4428 -- 149 2846 0.19 0.2284 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.3026
Anisotropic B[1][1] -3.3243
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.6923
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7006
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_dihedral_angle_d 14.569
f_chiral_restr 0.05
f_bond_d 0.005
f_angle_d 0.739
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3906
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 12

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.1.4
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.10