X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5
Temperature 289.0
Details 30% PEG300, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.73 α = 90
b = 128.73 β = 90
c = 165.15 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-10-01
CCD MARMOSAIC 225 mm CCD -- 2012-04-13
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9200 SSRF BL17U
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0063,1.0089,0.9791 SPring-8 BL41XU

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
3.15 50 99.6 -- -- -- -- 14541 14541 2.0 2.0 --
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)
3.15 50.0 99.5 -- -- -- -- --

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
MAD 3.15 39.168 -- 1.34 14541 14472 707 99.38 -- 0.2723 0.2714 0.29 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 3.15 3.3922 -- 143 2689 0.3359 0.3872 -- 100.0
X Ray Diffraction 3.3922 3.7334 -- 133 2707 0.3155 0.3461 -- 100.0
X Ray Diffraction 3.7334 4.273 -- 142 2729 0.2809 0.315 -- 100.0
X Ray Diffraction 4.273 5.3813 -- 146 2755 0.2622 0.2909 -- 100.0
X Ray Diffraction 5.3813 39.1706 -- 143 2885 0.2536 0.2496 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 65.7669
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.011
f_plane_restr 0.011
f_dihedral_angle_d 19.684
f_chiral_restr 0.112
f_angle_d 1.8
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3419
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.8_1069
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection
SOLVE phasing