X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.3
Temperature 300.0
Details protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3, 3 mM dehydroquinic acid, crystallization condition: 0.19 M sodium chloride, 17.9% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.7 α = 90
b = 64.27 β = 93.89
c = 81.04 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Bimorph K-B pair 2012-04-03
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 0.97850 APS 21-ID-D

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
1.62 30 97.2 0.054 -- -- 3.8 57849 57849 -- -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)
1.62 1.65 95.0 0.525 -- 2.6 3.6 2802

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 1.62 29.86 -- -- 54916 54916 2908 97.02 0.17531 0.17531 0.17349 0.20827 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 1.62 1.662 -- 214 3864 0.3 0.342 -- 93.47
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.376
Anisotropic B[1][1] 1.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.09
Anisotropic B[2][2] 1.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.33
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_gen_planes_refined 0.01
r_chiral_restr 0.12
r_dihedral_angle_4_deg 17.149
r_dihedral_angle_3_deg 11.983
r_dihedral_angle_2_deg 33.668
r_dihedral_angle_1_deg 4.216
r_angle_other_deg 0.862
r_angle_refined_deg 1.971
r_bond_other_d 0.001
r_bond_refined_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3750
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 359

Software

Computing
Computing Package Purpose
Blu Max Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
PHASER model building
Blu version: Max data collection