X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details 0.2 ul of 11 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azid, 0.5 mM TCEP, 7mM NADP and 20 mM tyrosine were mixed with 0.2 ul of the Index condition #83 (0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.41 α = 90
b = 68.89 β = 94.34
c = 51.1 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2013-06-20
Diffraction Radiation
Monochromator Protocol
Diamond [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 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
1.4 50 95.6 0.066 -- 21.868 2.3 -- 49774 0.0 -3.0 11.7
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 1.42 93.4 0.369 -- 1.8 1.7 2421

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
SAD 1.4 50.0 -- 0.0 -- 49707 2524 95.6 -- 0.1173 0.1151 0.1587 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 -- 186 3470 0.239 0.286 -- 95.23
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.987
Anisotropic B[1][1] 0.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.2
Anisotropic B[2][2] -0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.27
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 4.853
r_chiral_restr 0.108
r_bond_other_d 0.002
r_dihedral_angle_4_deg 14.731
r_dihedral_angle_2_deg 35.792
r_gen_planes_refined 0.008
r_sphericity_free 20.153
r_rigid_bond_restr 4.816
r_dihedral_angle_3_deg 12.019
r_angle_other_deg 1.634
r_sphericity_bonded 11.494
r_mcbond_other 1.801
r_mcangle_it 2.219
r_angle_refined_deg 1.616
r_gen_planes_other 0.006
r_bond_refined_d 0.014
r_mcbond_it 1.802
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2162
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 276

Software

Software
Software Name Purpose
Blu-Ice data collection
HKL-3000 data collection
HKL-3000 data reduction
HKL-3000 data scaling
HKL-3000 phasing
SHELX phasing
DM phasing
REFMAC refinement version: 5.8.0073
PDB_EXTRACT data extraction version: 3.15
SCALEPACK data scaling