X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8.5
Temperature 298.0
Details 30% PEG400, 0.05M CaCl2, 0.1M Bicine, pH 8.5, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 152.99 α = 90
b = 152.99 β = 90
c = 360.75 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2013-06-26
Diffraction Radiation
Monochromator Protocol
Si(III) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C

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
3.54 50 90.8 0.077 -- -- 2.9 18421 18421 2.0 2.0 127.17
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)
3.54 3.68 92.9 0.499 -- -- 2.9 2058

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 3.54 48.798 -- 1.36 18396 18396 961 90.68 -- 0.2824 0.2796 0.3331 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 3.5349 3.7212 -- 139 2525 0.3031 0.4081 -- 93.0
X Ray Diffraction 3.7212 3.9542 -- 143 2528 0.2779 0.3832 -- 93.0
X Ray Diffraction 3.9542 4.2594 -- 145 2527 0.2634 0.3982 -- 93.0
X Ray Diffraction 4.2594 4.6877 -- 123 2484 0.2391 0.3188 -- 91.0
X Ray Diffraction 4.6877 5.3653 -- 134 2511 0.26 0.3184 -- 91.0
X Ray Diffraction 5.3653 6.7569 -- 137 2489 0.34 0.4443 -- 90.0
X Ray Diffraction 6.7569 48.8024 -- 140 2371 0.2781 0.2734 -- 83.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 94.6161
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_chiral_restr 0.054
f_angle_d 0.794
f_plane_restr 0.003
f_dihedral_angle_d 16.123
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7667
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: 1.8.1_1168
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum
HKL-2000 data reduction
PHASER phasing