X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 298.0
Details PEG 1500, MIB buffer, pH 6.0, vapor diffusion, sitting drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 138.15 α = 90
b = 138.15 β = 90
c = 104.52 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Rayonix -- 2009-11-03
Diffraction Radiation
Monochromator Protocol
SILICON SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1

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
2.66 34.54 99.9 0.081 -- -- -- 33425 33394 -- -3.0 57.689
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)
2.66 2.73 100.0 0.679 -- 3.0 -- --

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 2.66 34.537 -- 1.99 -- 33390 1669 99.95 -- 0.2009 0.1983 0.2501 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 2.66 2.755 -- 166 3154 0.242 0.3304 -- 100.0
X Ray Diffraction 2.755 2.8653 -- 163 3096 0.2453 0.2974 -- 100.0
X Ray Diffraction 2.8653 2.9956 -- 167 3179 0.2582 0.3375 -- 100.0
X Ray Diffraction 2.9956 3.1535 -- 164 3116 0.2496 0.3338 -- 100.0
X Ray Diffraction 3.1535 3.3509 -- 165 3142 0.2275 0.3134 -- 100.0
X Ray Diffraction 3.3509 3.6094 -- 168 3174 0.1969 0.251 -- 100.0
X Ray Diffraction 3.6094 3.9721 -- 166 3162 0.1871 0.2426 -- 100.0
X Ray Diffraction 3.9721 4.5458 -- 168 3182 0.1598 0.2135 -- 100.0
X Ray Diffraction 4.5458 5.723 -- 168 3209 0.1512 0.1683 -- 100.0
X Ray Diffraction 5.723 34.537 -- 174 3307 0.1925 0.2384 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.3584
Anisotropic B[1][1] 3.6444
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.6444
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.2887
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.314
f_bond_d 0.008
f_chiral_restr 0.071
f_plane_restr 0.005
f_angle_d 1.132
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6052
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 115

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.1.4
PHENIX refinement version: 1.5_2
PDB_EXTRACT data extraction version: 3.10