X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.44 α = 90
b = 81.44 β = 90
c = 120.53 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU

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 50 99.6 0.051 -- -- 8.6 -- 27589 -- -- --
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 2.18 99.3 0.47 -- 5.2 8.8 --

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
SAD 2.1 50.0 -- -- -- 26173 1386 99.65 -- 0.22092 0.21863 0.2627 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 2.153 -- 109 1904 0.251 0.292 -- 98.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.548
Anisotropic B[1][1] 0.48
Anisotropic B[1][2] 0.24
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.72
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.126
r_xyhbond_nbd_refined 0.233
r_scbond_it 1.179
r_dihedral_angle_3_deg 13.4
r_gen_planes_refined 0.003
r_symmetry_hbond_refined 0.151
r_dihedral_angle_1_deg 5.447
r_chiral_restr 0.071
r_scangle_it 1.871
r_dihedral_angle_2_deg 35.915
r_mcbond_it 0.604
r_nbd_refined 0.181
r_bond_refined_d 0.007
r_nbtor_refined 0.297
r_symmetry_vdw_refined 0.149
r_dihedral_angle_4_deg 15.926
r_mcangle_it 1.064
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2614
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 230

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
SOLVE phasing