X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 300.0
Details protein: 7.5 mg/mL in 0.5 M sodium shikimate, 0.01 M Tris-HCl, crystallization condition: Qiagen PEG II B8 (0.01 M nickel chloride, 0.1 M Tris, pH 8.5, 20% w/v PEG2000 MME), crystal incubated in and frozen from 5 M sodium quinate, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.67 α = 90
b = 74.43 β = 100.57
c = 63.13 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 Beryllium lens 2012-07-20
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
1.78 30 97.2 0.056 -- -- 3.0 41378 41378 -- -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)
1.78 1.81 99.3 0.314 -- 2.4 2.3 2109

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 1.78 28.66 -- -- 39202 39202 2100 97.22 0.16079 0.16079 0.15927 0.18801 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 1.78 1.826 -- 154 2917 0.244 0.251 -- 99.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.88
Anisotropic B[1][1] 0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.42
Anisotropic B[2][2] -0.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.35
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.082
r_dihedral_angle_4_deg 12.821
r_dihedral_angle_3_deg 9.917
r_dihedral_angle_2_deg 33.743
r_dihedral_angle_1_deg 3.128
r_angle_other_deg 0.727
r_angle_refined_deg 1.351
r_bond_other_d 0.001
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3818
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 239

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