X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 300.0
Details protein: 7.5 mg/mL in 0.5 M sodium chloride, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG B6 (0.1 M MIB buffer, pH 9.0, 25% w/v PEG1500), 25 mM dehydroquinic acid crystal soak, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.84 α = 90
b = 71.67 β = 90
c = 171.76 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Beryllium lens 2012-06-18
Diffraction Radiation
Monochromator Protocol
diamond(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G

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
1.95 30 99.9 0.081 -- -- 7.1 34213 34213 -- -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)
1.95 1.98 99.9 0.611 -- 3.0 6.9 1655

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 1.95 28.63 -- -- 32362 32362 1746 99.82 0.19292 0.19292 0.18994 0.24735 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 1.95 2.0 -- -- 2329 0.26 0.306 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.952
Anisotropic B[1][1] -1.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.29
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.006
r_chiral_restr 0.085
r_dihedral_angle_4_deg 14.069
r_dihedral_angle_3_deg 10.691
r_dihedral_angle_2_deg 35.046
r_dihedral_angle_1_deg 3.152
r_angle_other_deg 0.728
r_angle_refined_deg 1.437
r_bond_other_d 0.001
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4002
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 243

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