X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 1.0M sodium/potassium tartrate, 0.1M Hepes, pH 7.0, vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.75 α = 90
b = 56.75 β = 90
c = 134.85 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 315r -- 2009-12-20
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.977 ESRF ID14-4

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
1.96 49.14 100.0 -- 0.103 -- 16.7 9923 9923 0.9 0.9 --
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)
1.96 2.06 100.0 0.724 0.724 0.9 16.7 1380

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 1.96 33.169 -- 0.0 9877 9877 476 99.96 0.2023 0.2023 0.2005 0.2394 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 1.96 2.2413 -- 176 3004 0.2368 0.2574 -- 100.0
X Ray Diffraction 2.2413 2.8235 -- 146 3092 0.1942 0.2252 -- 100.0
X Ray Diffraction 2.8235 33.1739 -- 154 3305 0.1944 0.2393 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.6202
Anisotropic B[1][1] 5.0643
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.0643
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -10.1286
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.512
f_plane_restr 0.002
f_chiral_restr 0.045
f_angle_d 0.797
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 862
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 40

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 3.3.16 data reduction
Mosflm data collection