X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 295.0
Details Protein: 7.1mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl pH 8.3, Screen: Trap96 (E8), 0.2M Ammonium sulfate, 0.1M Cacodyl. pH 6.5, 30% (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.9 α = 90
b = 126.9 β = 90
c = 115.58 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Beryllium lenses 2012-12-10
Diffraction Radiation
Monochromator Protocol
Diamond 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
2.6 30 99.6 0.063 -- -- 3.9 55066 55066 -- -3.0 69.9
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)
2.6 2.64 100.0 0.567 -- 2.4 3.9 2698

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 2.6 29.91 -- -- 26680 26680 1414 99.87 0.17317 0.17317 0.17096 0.215 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 2.601 2.668 1894 100 1894 0.263 0.348 -- 98.62
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Thermal Factors Individually Isotropically Refined
Mean Isotropic B 54.203
Anisotropic B[1][1] -0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.34
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.566
r_scbond_it 2.969
r_mcangle_it 1.833
r_mcbond_other 0.232
r_bond_refined_d 0.011
r_bond_other_d 0.001
r_angle_refined_deg 1.304
r_angle_other_deg 0.794
r_dihedral_angle_1_deg 2.575
r_dihedral_angle_2_deg 33.549
r_dihedral_angle_3_deg 11.109
r_dihedral_angle_4_deg 19.279
r_chiral_restr 0.078
r_gen_planes_refined 0.005
r_gen_planes_other 0.001
r_mcbond_it 0.974
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4836
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 188

Software

Computing
Computing Package Purpose
Blu Max Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHENIX Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0102 refinement
PHENIX model building
Blu version: Max data collection