X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
Temperature 293.0
Details PEG3350, Salt

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 138.02 α = 90
b = 138.02 β = 90
c = 157.97 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 300K -- 2017-11-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL12B2 0.9785 SPring-8 BL12B2

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
3 104.15 94.6 -- -- -- 5.7 -- 29350 -- -- --
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)
3.0 3.18 96.7 0.963 -- 1.3 5.6 --

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 3.0 104.15 -- -- -- 27826 1430 93.84 -- 0.2357 0.23362 0.27551 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 3.0 3.078 -- 106 2054 0.378 0.42 -- 96.34
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 86.632
Anisotropic B[1][1] 1.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.47
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.157
r_bond_refined_d 0.006
r_bond_other_d 0.002
r_mcbond_other 0.789
r_dihedral_angle_2_deg 33.734
r_scbond_it 0.657
r_gen_planes_other 0.001
r_scangle_other 1.249
r_long_range_B_refined 2.993
r_scbond_other 0.655
r_dihedral_angle_1_deg 6.057
r_chiral_restr 0.063
r_mcangle_other 1.46
r_long_range_B_other 2.993
r_angle_other_deg 0.835
r_dihedral_angle_3_deg 13.56
r_mcangle_it 1.46
r_dihedral_angle_4_deg 16.467
r_gen_planes_refined 0.004
r_mcbond_it 0.789
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6017
Nucleic Acid Atoms 0
Heterogen Atoms 181
Solvent Atoms 2

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
MOSFLM data reduction
Aimless data scaling
PHASER phasing