X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 1.0M LiCl, 0.1M TRIS pH8.0, 20% PEG6K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.41 α = 90
b = 97.41 β = 90
c = 80.66 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 92 VariMax HF 2012-10-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 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
2.1 30 98.2 0.079 -- -- 4.2 -- 25440 -- -- --
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)
2.1 2.18 97.3 0.44 -- 3.3 4.1 --

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 2.1 28.12 -- -- -- 23693 1269 98.23 -- 0.18135 0.17926 0.22114 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 2.102 2.156 -- 73 1735 0.232 0.311 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 42.691
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] -0.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.23
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 35.023
r_scangle_other 2.72
r_mcbond_it 1.59
r_long_range_B_other 4.477
r_chiral_restr 0.062
r_scbond_it 1.611
r_mcbond_other 1.591
r_gen_planes_refined 0.004
r_mcangle_it 2.556
r_angle_refined_deg 1.053
r_scbond_other 1.61
r_dihedral_angle_1_deg 4.958
r_angle_other_deg 0.709
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 12.958
r_dihedral_angle_4_deg 13.045
r_bond_refined_d 0.006
r_bond_other_d 0.001
r_long_range_B_refined 4.647
r_mcangle_other 2.555
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2225
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 164

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0049
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing