X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 289.0
Details 0.2 ul of mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the Hampton Index HT #65 (F5) (0.1 M Ammonium acetate, 0.1 M BIS_TRIS pH 5.5, 17% (w/v) Polyethylene glycol 10,000) and equilibrated against 1.25 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 = 81.64 α = 90
b = 128.47 β = 116.36
c = 84.47 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 ADSC QUANTUM 210r -- 2013-11-14
Diffraction Radiation
Monochromator Protocol
Si [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97936 APS 19-BM

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
1.82 50 99.5 0.104 -- 18.06 4.7 -- 138544 -- -- --
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)
1.82 1.85 93.8 -- -- -- 3.6 6515

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 1.82 50.0 -- 0.0 -- 138432 6926 99.16 -- 0.1685 0.1672 0.1926 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 1.82 1.867 -- 469 8864 0.312 0.322 -- 90.71
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.527
Anisotropic B[1][1] 1.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.09
Anisotropic B[2][2] -0.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.5
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.74
r_chiral_restr 0.059
r_bond_refined_d 0.005
r_dihedral_angle_1_deg 5.015
r_dihedral_angle_3_deg 11.17
r_gen_planes_other 0.001
r_dihedral_angle_4_deg 16.405
r_gen_planes_refined 0.003
r_angle_other_deg 0.713
r_mcbond_it 0.74
r_mcangle_it 1.253
r_angle_refined_deg 1.008
r_bond_other_d 0.001
r_dihedral_angle_2_deg 32.921
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 0
Solvent Atoms 1491

Software

Software
Software Name Purpose
HKL-3000 data scaling
REFMAC refinement version: 5.8.0073
PDB_EXTRACT data extraction version: 3.15
HKL-3000 data collection
DENZO data reduction
SCALEPACK data scaling
SHELXD phasing