X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 20% PEG 3350, 0.2M sodium acetate, 0.1M Bis Tris propane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.04 α = 90
b = 83.25 β = 90
c = 170.35 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 RAYONIX MX-225 mirrors 2012-01-31
Diffraction Radiation
Monochromator Protocol
silicon SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 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
3.1 46.9 99.6 0.241 -- -- 9.0 18422 18422 0.0 0.0 23.07
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)
3.1 3.27 98.2 0.596 -- 1.2 7.1 2548

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 3.1 38.802 -- 0.0 -- 17704 912 95.97 -- 0.2979 0.2952 0.3469 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 3.1001 3.2634 -- 143 2165 0.3554 0.4535 -- 90.0
X Ray Diffraction 3.2634 3.4678 -- 134 2323 0.3201 0.4235 -- 95.0
X Ray Diffraction 3.4678 3.7353 -- 130 2358 0.2896 0.364 -- 96.0
X Ray Diffraction 3.7353 4.1109 -- 117 2419 0.2938 0.3249 -- 97.0
X Ray Diffraction 4.1109 4.7048 -- 132 2458 0.2787 0.3164 -- 98.0
X Ray Diffraction 4.7048 5.9242 -- 135 2452 0.2851 0.3025 -- 97.0
X Ray Diffraction 5.9242 38.805 -- 121 2617 0.2722 0.2739 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.3983
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.328
f_plane_restr 0.006
f_chiral_restr 0.087
f_angle_d 1.484
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6312
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
RAYONIX MX225HE Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
molrep Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1069) refinement
molrep model building
RAYONIX version: MX225HE data collection