X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details 1.6M SODIUM CITRATE TRIBASIC

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.44 α = 90
b = 73.44 β = 90
c = 158.2 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r X-RAY FLUORESCCENCE DETECTOR 2014-06-27
Diffraction Radiation
Monochromator Protocol
CRYOGENICALLY COOLED CHANNEL-CUT SI[111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 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
2.24 50 99.5 0.062 -- -- 6.9 -- 24436 -- -3.0 49.9
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)
2.24 2.37 98.6 0.633 -- 2.95 -- --

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 2.24 36.718 -- 1.38 -- 24436 1905 99.73 -- 0.2268 0.2241 0.2588 Random selection
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 2.24 2.296 -- 136 1604 0.3168 0.3815 -- 100.0
X Ray Diffraction 2.296 2.3581 -- 133 1568 0.2992 0.3533 -- 100.0
X Ray Diffraction 2.3581 2.4275 -- 134 1580 0.2788 0.3145 -- 100.0
X Ray Diffraction 2.4275 2.5058 -- 136 1582 0.2885 0.3455 -- 100.0
X Ray Diffraction 2.5058 2.5954 -- 134 1584 0.2736 0.3266 -- 100.0
X Ray Diffraction 2.5954 2.6992 -- 135 1596 0.2609 0.3185 -- 100.0
X Ray Diffraction 2.6992 2.822 -- 140 1612 0.2564 0.3434 -- 100.0
X Ray Diffraction 2.822 2.9708 -- 135 1571 0.2481 0.3184 -- 100.0
X Ray Diffraction 2.9708 3.1568 -- 132 1606 0.2465 0.3166 -- 100.0
X Ray Diffraction 3.1568 3.4004 -- 132 1616 0.2253 0.2806 -- 100.0
X Ray Diffraction 3.4004 3.7423 -- 136 1633 0.1978 0.2501 -- 100.0
X Ray Diffraction 3.7423 4.2831 -- 133 1632 0.1904 0.1851 -- 100.0
X Ray Diffraction 4.2831 5.3935 -- 141 1653 0.1836 0.2014 -- 100.0
X Ray Diffraction 5.3935 36.7234 -- 148 1694 0.2347 0.2472 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.45
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.087
f_bond_d 0.009
f_angle_d 1.204
f_dihedral_angle_d 13.937
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2097
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 163

Software

Software
Software Name Purpose
PHENIX refinement
XSCALE data scaling
PHASER phasing version: 2.5.2
PDB_EXTRACT data extraction version: 3.15
XDS data reduction