X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.5
Temperature 277.0
Details 0.1 M NaCl, 0.1 M CAPSO pH 9.5, 0.175 M LiSO4, 14% PEG 4000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.29 α = 90
b = 75.29 β = 90
c = 71.38 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F KB mirrors 2015-10-01
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976252 PETRA III, EMBL c/o DESY P13 (MX1)

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
1.86 65.2 94.4 -- 0.027 -- 3.89 -- 18191 -- -- --
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)
1.86 1.98 78.9 -- -- 3.37 3.07 --

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 1.86 65.2 -- -- -- 17263 921 94.33 -- 0.19596 0.1941 0.22872 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 1.864 1.912 -- 35 788 0.332 0.347 -- 58.24
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.426
Anisotropic B[1][1] 0.53
Anisotropic B[1][2] 0.26
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.71
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 34.767
r_mcbond_it 3.492
r_gen_planes_refined 0.013
r_dihedral_angle_4_deg 15.857
r_mcangle_other 4.393
r_dihedral_angle_3_deg 12.798
r_bond_refined_d 0.02
r_long_range_B_refined 8.03
r_bond_other_d 0.005
r_angle_refined_deg 2.376
r_chiral_restr 0.144
r_mcangle_it 4.394
r_gen_planes_other 0.02
r_scbond_it 4.414
r_long_range_B_other 8.055
r_dihedral_angle_1_deg 6.737
r_angle_other_deg 1.48
r_mcbond_other 3.49
r_scangle_other 6.544
r_scbond_other 4.411
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1304
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 67

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0131
XDS data reduction
PHASER phasing