X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.0
Details 0.1M HEPES pH7.5, 0.2M NaCl, 40% PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 230.33 α = 90
b = 230.33 β = 90
c = 230.33 γ = 90
Symmetry
Space Group I 4 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 35
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2010-11-01
Diffraction Radiation
Monochromator Protocol
Double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.97923 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
3.5 81.4 100.0 0.125 0.125 -- 11.5 13479 13479 0.0 0.0 11.9
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)
3.5 3.69 100.0 0.242 -- 10.4 11.8 1913

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 3.5 72.836 -- 1.5 13465 13465 665 99.88 -- 0.1812 0.1794 0.2155 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 3.5003 3.7705 -- 115 2516 0.1987 0.2511 -- 100.0
X Ray Diffraction 3.7705 4.1499 -- 135 2504 0.1793 0.246 -- 100.0
X Ray Diffraction 4.1499 4.7503 -- 149 2512 0.1475 0.1733 -- 100.0
X Ray Diffraction 4.7503 5.9845 -- 120 2577 0.1758 0.2258 -- 100.0
X Ray Diffraction 5.9845 72.8518 -- 146 2691 0.1982 0.2066 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.735
f_bond_d 0.004
f_chiral_restr 0.046
f_plane_restr 0.003
f_dihedral_angle_d 15.114
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4178
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
SPring-8 data collection version: BBS
PHENIX model building
PHENIX refinement version: (phenix.refine: 1.7.1_743)
MOSFLM data reduction
SCALA data scaling
PHENIX phasing