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 12 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 MCSG Suite 3 condition #81 (0.2M NaCl, 0.1M Na citrate, 40%v/v 1,2-propanodiol pH=5.5) 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 = 105.11 α = 90
b = 105.11 β = 90
c = 479.57 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2014-07-23
Diffraction Radiation
Monochromator Protocol
Si [111] SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID

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
1.9 50 100.0 0.082 0.082 20.094 5.9 106320 106320 -- -3.0 27.3
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)
1.9 1.93 100.0 0.83 -- 1.9 5.8 5256

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 1.9 50.0 -- 0.0 -- 100839 5293 99.93 -- 0.1617 0.1605 0.1847 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 1.9 1.949 -- 391 7350 0.238 0.251 -- 99.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.569
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.009
r_mcbond_other 1.329
r_dihedral_angle_4_deg 17.86
r_chiral_restr 0.071
r_mcangle_it 2.14
r_gen_planes_other 0.005
r_angle_other_deg 2.269
r_dihedral_angle_3_deg 12.719
r_angle_refined_deg 1.261
r_gen_planes_refined 0.006
r_mcbond_it 1.329
r_bond_other_d 0.002
r_dihedral_angle_2_deg 35.188
r_dihedral_angle_1_deg 5.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7159
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 964

Software

Software
Software Name Purpose
HKL-3000 data collection
HKL-3000 data reduction
HKL-3000 data scaling
HKL-3000 phasing
MOLREP phasing
Coot model building
REFMAC refinement version: 5.8.0049
PDB_EXTRACT data extraction version: 3.15