X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.8
Temperature 293.0
Details 50 mM NaCl, 0.3 mM tris(2-carboxyethyl)phosphine, 10 mM HEPES-NaOH (pH 7.8), 20% polyethylene glycol 3350, 200 mM sodium formate, 40 mM glycine, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 104.23 α = 90
b = 104.23 β = 90
c = 115.31 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 MARMOSAIC 300 mm CCD -- 2011-12-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.1271 APS 21-ID-D

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
2.42 50 100.0 0.107 -- -- 10.5 -- 9427 -- -- --
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)
2.45 2.49 100.0 0.872 -- -- 10.0 --

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 2.416 48.591 -- 0.0 -- 8976 905 95.17 -- 0.1846 0.1795 0.2294 --
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 2.4164 2.5678 -- 137 1208 0.2551 0.3246 -- 87.0
X Ray Diffraction 2.5678 2.7661 -- 145 1275 0.2273 0.3514 -- 91.0
X Ray Diffraction 2.7661 3.0444 -- 148 1331 0.2283 0.2911 -- 96.0
X Ray Diffraction 3.0444 3.4848 -- 154 1378 0.2045 0.3041 -- 98.0
X Ray Diffraction 3.4848 4.39 -- 157 1404 0.1642 0.2085 -- 99.0
X Ray Diffraction 4.39 48.6005 -- 164 1475 0.1494 0.1696 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.2611
Anisotropic B[1][1] 9.9895
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.9895
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -19.9789
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.048
f_dihedral_angle_d 20.074
f_angle_d 0.845
f_bond_d 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1357
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 74

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
phenix Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
RESOLVE version: 2.15 density modification
HKL data reduction