X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 278.0
Details 0.1 M MES, pH 5.5, 10 % (w/v) PEG 6000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.24 α = 90
b = 146.24 β = 90
c = 67.44 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2015-12-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.033 ESRF ID23-1

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
2.9 103.4 99.8 0.05 -- -- 2.0 -- 16737 -- -- --
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)
2.9 3.0 -- -- -- -- -- --

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 2.9 61.2 -- -- -- 16201 536 99.81 -- 0.15915 0.15727 0.21229 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 2.9 2.975 -- 43 1182 0.237 0.29 -- 99.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.759
Anisotropic B[1][1] -1.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.91
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_refined 4.66
r_bond_refined_d 0.01
r_dihedral_angle_2_deg 35.528
r_dihedral_angle_4_deg 15.581
r_angle_refined_deg 1.507
r_dihedral_angle_1_deg 6.408
r_mcbond_other 1.571
r_mcangle_it 2.68
r_gen_planes_other 0.001
r_chiral_restr 0.084
r_bond_other_d 0.002
r_angle_other_deg 1.049
r_mcbond_it 1.574
r_scangle_other 2.711
r_mcangle_other 2.68
r_dihedral_angle_3_deg 15.783
r_scbond_other 1.588
r_long_range_B_other 4.66
r_scbond_it 1.588
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4028
Nucleic Acid Atoms 568
Heterogen Atoms 37
Solvent Atoms 111

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0123
XDS data reduction
SCALA data scaling
PHASER phasing