X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 289.0
Details 0.2 ul of 14 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 2 condition #28 (0.2 M Ammonium Citrate Tribasic pH 7.0, 20% (w/v) PEG 3350) 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 1 mg/ml TEV solution at 289 K for 1 hour

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.05 α = 90
b = 78.67 β = 90
c = 79.54 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 Lenses 2015-04-16
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
1.3 50 99.9 0.052 0.02 29.917 5.9 68811 68759 -- -3.0 12.1
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)
1.3 1.32 100.0 0.67 -- 2.1 5.4 3380

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 1.3 50.0 -- 0.0 -- 65197 3483 99.9 -- 0.1165 0.1152 0.1401 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 1.3 1.334 -- 235 4814 0.211 0.221 -- 99.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.157
Anisotropic B[1][1] 0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.009
r_angle_refined_deg 1.46
r_dihedral_angle_2_deg 34.524
r_rigid_bond_restr 1.249
r_sphericity_free 24.475
r_chiral_restr 0.082
r_sphericity_bonded 11.664
r_mcangle_it 1.705
r_mcbond_it 1.332
r_angle_other_deg 1.966
r_bond_other_d 0.002
r_dihedral_angle_3_deg 11.076
r_gen_planes_other 0.004
r_mcbond_other 1.332
r_dihedral_angle_4_deg 16.474
r_gen_planes_refined 0.007
r_dihedral_angle_1_deg 5.461
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2107
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 432

Software

Software
Software Name Purpose
PDB_EXTRACT data extraction version: 3.15
REFMAC refinement version: 5.8.0107
HKL-3000 phasing
MLPHARE phasing
SHELX phasing
HKL-3000 data scaling
HKL-3000 data reduction
BLU-MAX data collection