X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 2.1 M ammonium sulfate, 100 mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.62 α = 90
b = 92.62 β = 90
c = 173.17 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 MARMOSAIC 325 mm CCD bent Si-mirror 2006-05-18
Diffraction Radiation
Monochromator Protocol
diamond (111) double-crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2

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
1.7 46.8 99.6 0.08 -- -- 5.7 94781 94781 0.0 0.0 38.2
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)
1.7 1.76 100.0 0.34 -- 3.2 5.3 9332

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
FOURIER SYNTHESIS 1.8 38.1 -- 0.0 76024 76024 4015 99.62 0.18523 0.18523 0.1832 0.22348 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 1.8 1.847 5563 297 5563 0.258 0.322 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.766
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_gen_planes_refined 0.009
r_chiral_restr 0.121
r_dihedral_angle_4_deg 19.399
r_dihedral_angle_3_deg 15.728
r_dihedral_angle_2_deg 35.874
r_dihedral_angle_1_deg 6.536
r_angle_other_deg 0.933
r_angle_refined_deg 1.96
r_bond_other_d 0.001
r_bond_refined_d 0.019
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.217
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5690
Nucleic Acid Atoms 0
Heterogen Atoms 137
Solvent Atoms 465

Software

Computing
Computing Package Purpose
Blu-ice Data Collection
CrystalClear Data Reduction (intensity integration)
CrystalClear Data Reduction (data scaling)
Refmac5 Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
Refmac5 model building
Blu-ice data collection