X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.15
Details 0.1 M HEPES pH 7.5, 20% PEG 10000, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.03 α = 90
b = 29.67 β = 116.41
c = 62 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR RIGAKU RAXIS IV++ -- 2011-01-20
Diffraction Radiation
Monochromator Protocol
Ni Filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.541 -- --

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
1.85 23.41 96.4 -- -- -- -- 12091 12091 0.0 -3.0 25.16
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)
1.85 1.92 81.1 -- -- -- -- --

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 1.85 23.413 -- 0.0 12091 12073 580 96.23 -- 0.2058 0.2038 0.2439 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 1.85 2.0361 -- 144 2667 0.2898 0.3932 -- 91.0
X Ray Diffraction 2.0361 2.3305 -- 156 2932 0.2061 0.2511 -- 99.0
X Ray Diffraction 2.3305 2.9353 -- 129 2977 0.2031 0.2705 -- 99.0
X Ray Diffraction 2.9353 23.4144 -- 151 2917 0.1886 0.2066 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.1275
Anisotropic B[1][1] -3.3304
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.231
Anisotropic B[2][2] -5.0827
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.413
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_bond_d 0.007
f_dihedral_angle_d 14.919
f_angle_d 1.06
f_chiral_restr 0.071
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1061
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 161

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.6.4_486) Structure Refinement
Software
Software Name Purpose
Phaser molecular replacement
phenix refinement
pdb_extract version: 3.11 data extraction