X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details 5 mM cobalt chloride, 5 mM cadmium chloride, 5 mM magnesium chloride, 5 mM nickel chloride, 0.1 M HEPES pH 7.5, 12 % PEG 3350.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.16 α = 90
b = 80.57 β = 90
c = 109.69 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 S 6M -- 2017-12-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 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
1.5 65 99.9 -- -- -- 5.4 -- 81571 -- -- --
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)
1.5 1.53 -- -- -- -- -- --

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 1.5 64.94 -- -- -- 81571 4265 99.85 -- 0.17552 0.17428 0.19955 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 1.5 1.539 -- 317 5927 0.311 0.31 -- 99.9
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.012
Anisotropic B[1][1] -0.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.08
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_other 3.918
r_angle_refined_deg 1.508
r_angle_other_deg 0.782
r_dihedral_angle_2_deg 32.961
r_gen_planes_other 0.002
r_scbond_other 4.541
r_dihedral_angle_3_deg 13.235
r_bond_refined_d 0.013
r_dihedral_angle_1_deg 11.111
r_long_range_B_refined 8.581
r_long_range_B_other 8.363
r_gen_planes_refined 0.015
r_mcbond_it 2.874
r_dihedral_angle_4_deg 20.309
r_scangle_other 6.574
r_scbond_it 4.549
r_bond_other_d 0.001
r_mcbond_other 2.875
r_mcangle_it 3.919
r_chiral_restr 0.123
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3142
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 589

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0189
XDS data reduction
Aimless data scaling
MOLREP phasing