X-RAY DIFFRACTION Experimental Data & Validation


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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 = 92.24 α = 90
b = 92.24 β = 90
c = 172.87 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 ADSC QUANTUM 315 bent Si-mirror 2006-04-16
Diffraction Radiation
Monochromator Protocol
bent Ge(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.9002 APS 14-BM-C

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
1.4 39 99.5 0.07 -- -- 7.1 166757 166757 0.0 0.0 23.0
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)
1.4 1.45 99.5 0.328 -- 3.8 5.8 16554

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 1.4 38.92 -- 0.0 -- 158418 8318 99.52 -- 0.18273 0.18003 0.23413 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 1.4 1.436 11155 560 11155 0.348 0.396 -- 99.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.841
Anisotropic B[1][1] 0.81
Anisotropic B[1][2] 0.4
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.81
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.21
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 15.429
r_sphericity_free 38.476
r_bond_refined_d 0.018
r_bond_other_d 0.002
r_angle_refined_deg 1.941
r_angle_other_deg 1.084
r_dihedral_angle_1_deg 7.691
r_dihedral_angle_2_deg 34.732
r_dihedral_angle_3_deg 13.114
r_dihedral_angle_4_deg 19.515
r_chiral_restr 0.123
r_gen_planes_refined 0.01
r_gen_planes_other 0.002
r_rigid_bond_restr 5.608
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.228
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5690
Nucleic Acid Atoms 0
Heterogen Atoms 152
Solvent Atoms 561

Software

Computing
Computing Package Purpose
XDISPLAYF Data Collection
d*TREK Data Reduction (intensity integration)
CrystalClear Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
Molrep model building
XDISPLAYF data collection