X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details Bis-Tris propan, CaCl2, PEG3350, pH 6.0, vapor diffusion, sitting drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.53 α = 90
b = 96.53 β = 90
c = 300.39 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2011-11-12
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.97906 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
4.18 48.79 98.8 0.121 -- -- -- -- 12539 -- -3.0 168.154
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)
4.18 4.43 94.0 0.956 -- 2.48 -- --

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
-- 4.18 42.952 -- -- -- 12524 875 98.85 -- 0.295 0.2922 0.3348 --
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 4.18 4.4405 -- 129 1782 0.3491 0.3706 -- 94.0
X Ray Diffraction 4.4405 4.7829 -- 152 1930 0.3276 0.3402 -- 100.0
X Ray Diffraction 4.7829 5.2635 -- 140 1936 0.3147 0.3987 -- 100.0
X Ray Diffraction 5.2635 6.0233 -- 137 1968 0.3146 0.3542 -- 100.0
X Ray Diffraction 6.0233 7.5819 -- 167 1957 0.313 0.3166 -- 100.0
X Ray Diffraction 7.5819 42.9538 -- 150 2076 0.2588 0.3161 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 135.033
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.144
f_plane_restr 0.003
f_chiral_restr 0.036
f_angle_d 0.807
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8128
Nucleic Acid Atoms 3102
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
BSS Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.2_1309) Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction