X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details 200mM calcium acetate, 100mM imidazole/ hydrochloric acid pH 8.0, and 20%(w/v) PEG 1000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.08 α = 90
b = 123.34 β = 107.88
c = 101.38 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 270 -- 2015-06-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A

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 46.73 97.9 0.068 -- -- 3.9 -- 86780 -- -- --
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 97.9 0.57 -- 2.2 2.8 --

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 46.73 -- -- -- 82451 4328 97.76 -- 0.17966 0.17763 0.21936 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 2.099 2.154 -- 294 5905 0.282 0.334 -- 94.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.02
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 13.965
r_scangle_other 3.168
r_dihedral_angle_2_deg 36.073
r_bond_refined_d 0.011
r_scbond_it 2.038
r_mcbond_it 1.713
r_long_range_B_other 4.25
r_angle_refined_deg 1.478
r_dihedral_angle_1_deg 7.059
r_long_range_B_refined 4.25
r_gen_planes_other 0.002
r_mcbond_other 1.713
r_dihedral_angle_4_deg 19.084
r_mcangle_other 2.507
r_mcangle_it 2.508
r_scbond_other 2.037
r_angle_other_deg 0.948
r_bond_other_d 0.003
r_chiral_restr 0.084
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11325
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 526

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
XDS data reduction
Aimless data scaling
BUCCANEER model building
MOLREP phasing