X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 0.1 M Bis-Tris propane pH 6.5, 16% w/v PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.57 α = 90
b = 65.57 β = 90
c = 63.47 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS HTC varimax confocal optics 2011-03-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ DW 1.54 -- --

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 50 99.8 0.125 -- -- 3.1 20700 20659 -- -3.0 --
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)
2.0 2.07 99.9 0.532 -- -- 3.1 2078

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 2.2 32.79 -- 0.0 15495 13875 715 89.55 -- 0.1982 0.1954 0.249 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 2.2 2.257 -- 53 863 0.239 0.35 -- 82.08
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.802
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] -0.06
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.06
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.19
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_dihedral_angle_2_deg 35.826
r_dihedral_angle_3_deg 12.073
r_angle_refined_deg 0.872
r_gen_planes_refined 0.003
r_dihedral_angle_1_deg 5.101
r_chiral_restr 0.053
r_angle_other_deg 0.703
r_gen_planes_other 0.001
r_bond_refined_d 0.005
r_dihedral_angle_4_deg 15.574
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2211
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 175

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
CrystalClear data collection
DENZO data reduction