X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 7% PEG 8000, 0.1M IMIDAZOLE, pH 8.0, vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.6 α = 90
b = 82.67 β = 90
c = 116.91 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 -- 2011-02-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
2.36 40 89.5 0.135 -- -- 3.2 -- 27781 -- -- --
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)
2.36 2.4 89.6 0.505 -- -- 2.2 1367

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 2.743 26.593 -- 1.34 -- 19151 950 95.66 -- 0.1826 0.179 0.2513 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 2.743 2.8874 -- 133 2521 0.2425 0.343 -- 95.0
X Ray Diffraction 2.8874 3.068 -- 156 2589 0.2269 0.306 -- 97.0
X Ray Diffraction 3.068 3.3045 -- 129 2600 0.2005 0.296 -- 97.0
X Ray Diffraction 3.3045 3.6363 -- 135 2629 0.1839 0.2803 -- 97.0
X Ray Diffraction 3.6363 4.1607 -- 135 2591 0.1692 0.2359 -- 96.0
X Ray Diffraction 4.1607 5.2355 -- 124 2593 0.1356 0.1862 -- 94.0
X Ray Diffraction 5.2355 26.593 -- 138 2678 0.1677 0.2134 -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.217
Anisotropic B[1][1] -5.6991
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.8888
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 12.5879
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_chiral_restr 0.072
f_angle_d 1.122
f_dihedral_angle_d 14.471
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5189
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 172

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.1.4
PHENIX refinement version: 1.7.3_928
PDB_EXTRACT data extraction version: 3.11
StructureStudio data collection