X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 282.0
Details 0.1 M Magnesium formate, 15% w/v Polyethylene glycol 3350, and 6% w/v 1,6-Hexanediol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.09 α = 90
b = 76.06 β = 90
c = 131.9 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 80
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2018-01-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.078 APS 21-ID-D

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
1.7 65.98 96.1 -- -- -- 14.0 -- 59837 -- -- --
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)
1.7 1.725 -- -- -- -- -- --

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 1.7 65.98 -- -- -- 56811 2991 96.09 -- 0.15692 0.1547 0.19868 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 1.696 1.74 -- 215 4105 0.219 0.267 -- 94.2
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.757
Anisotropic B[1][1] 0.9
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.48
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.7
r_dihedral_angle_1_deg 6.75
r_dihedral_angle_4_deg 21.547
r_gen_planes_refined 0.009
r_mcangle_other 2.584
r_mcangle_it 2.582
r_mcbond_it 1.748
r_scangle_other 4.339
r_gen_planes_other 0.001
r_bond_refined_d 0.013
r_scbond_it 2.876
r_long_range_B_other 5.216
r_chiral_restr 0.084
r_mcbond_other 1.747
r_angle_other_deg 1.07
r_dihedral_angle_2_deg 39.475
r_dihedral_angle_3_deg 15.16
r_long_range_B_refined 5.216
r_bond_other_d 0.001
r_scbond_other 2.875
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5564
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 439

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0230
XDS data scaling
PHENIX model building
BUCCANEER model building
PHENIX phasing
XDS data reduction