X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.2
Details 10% PEG6000, 0.1 M Na citrate, pH 4 and 1 M LiCl, vapor diffusion, sitting drop, temperature 293.2K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 129.59 α = 90
b = 129.59 β = 90
c = 536.89 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 -- 2011-06-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B

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 45 94.6 0.118 -- -- 9.2 -- 30241 -- -- --
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 3.21 63.0 0.315 -- -- 5.9 1985

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 3.106 41.898 -- 0.0 -- 27299 1373 85.41 -- 0.1953 0.1925 0.2505 --
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 3.1058 3.2168 -- 24 361 0.2591 0.247 -- 12.0
X Ray Diffraction 3.2168 3.3456 -- 79 1326 0.2514 0.3519 -- 45.0
X Ray Diffraction 3.3456 3.4977 -- 141 2882 0.2632 0.3455 -- 96.0
X Ray Diffraction 3.4977 3.6821 -- 161 3001 0.2282 0.2833 -- 100.0
X Ray Diffraction 3.6821 3.9126 -- 162 2994 0.2056 0.2594 -- 100.0
X Ray Diffraction 3.9126 4.2144 -- 140 3036 0.1797 0.2393 -- 100.0
X Ray Diffraction 4.2144 4.638 -- 162 3027 0.1513 0.2091 -- 100.0
X Ray Diffraction 4.638 5.308 -- 173 3032 0.152 0.2199 -- 100.0
X Ray Diffraction 5.308 6.6832 -- 165 3076 0.182 0.2291 -- 100.0
X Ray Diffraction 6.6832 41.9022 -- 166 3191 0.1851 0.2312 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.0562
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.998
f_plane_restr 0.004
f_chiral_restr 0.053
f_angle_d 0.753
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7211
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 0

Software

Computing
Computing Package Purpose
bluice Data Collection
DENZO Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1063) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
HKL data reduction
DENZO data collection