X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 295.0
Details protein - 9.6 mg/mL in 10 mM Tris-HCl pH 8.3, 250 mM NaCl, 5 mM BME, crystallization - The Classics II Suite C4 (28): 560 mM Sodium citrate pH 7.0, cryo - 25% (v/v) sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.94 α = 90
b = 85.63 β = 90
c = 93.67 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD Be lenses 2014-07-21
Diffraction Radiation
Monochromator Protocol
Diamond SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.1 30 95.1 0.063 -- -- 7.2 14651 14651 -- -3.0 40.5
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)
2.1 2.14 100.0 0.41 -- 5.3 7.4 746

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 2.1 28.9 -- -- 13578 13578 717 92.1 -- 0.21315 0.21094 0.25648 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 2.1 2.158 969 47 969 0.228 0.339 -- 90.96
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 54.647
Anisotropic B[1][1] 0.78
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.01
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.099
r_dihedral_angle_3_deg 14.608
r_gen_planes_refined 0.009
r_bond_refined_d 0.012
r_angle_other_deg 0.977
r_dihedral_angle_2_deg 35.586
r_gen_planes_other 0.004
r_angle_refined_deg 1.569
r_bond_other_d 0.004
r_dihedral_angle_1_deg 3.56
r_dihedral_angle_4_deg 11.593
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1727
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 78

Software

Software
Software Name Purpose
Blu-Ice data collection version: Max
PHASER phasing
REFMAC refinement version: 5.7.0029
HKL-3000 data reduction
HKL-3000 data scaling