X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 0.9M succinic acid pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.3 α = 90
b = 74.3 β = 90
c = 123.57 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 -- 2011-07-23
Diffraction Radiation
Monochromator Protocol
double crystal monochromator 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
2.2 50 100.0 0.086 -- -- 11.1 20524 20524 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)
2.2 2.24 99.2 0.491 -- 6.5 10.1 1006

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 2.201 34.692 -- 1.34 20524 20273 1035 98.29 0.2044 0.2044 0.2022 0.2456 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 2.2011 2.3171 -- 137 2663 0.3254 0.3655 -- 96.0
X Ray Diffraction 2.3171 2.4622 -- 167 2666 0.2949 0.3779 -- 99.0
X Ray Diffraction 2.4622 2.6523 -- 148 2741 0.2507 0.2867 -- 99.0
X Ray Diffraction 2.6523 2.9191 -- 143 2736 0.2502 0.3112 -- 99.0
X Ray Diffraction 2.9191 3.3412 -- 145 2771 0.2176 0.2728 -- 100.0
X Ray Diffraction 3.3412 4.2083 -- 152 2815 0.1859 0.2291 -- 100.0
X Ray Diffraction 4.2083 34.6962 -- 143 2846 0.1713 0.207 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 15.6664
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 15.6664
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -31.3328
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.078
f_dihedral_angle_d 16.606
f_angle_d 1.036
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2107
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 23

Software

Computing
Computing Package Purpose
Bluice Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
Bluice data collection