X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details 100 mM MES pH 6.0-6.5, 100-200 mM NaCl, 32-36% PEG400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.67 α = 86.1
b = 91.87 β = 82.22
c = 96.32 γ = 69.66
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 130 mm -- 2016-11-23
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.979 PAL/PLS 7A (6B, 6C1)

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
3.76 95.41 99.2 -- -- -- 1.9 -- 26874 -- -- --
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)
3.8 3.9 98.6 -- -- -- 1.9 --

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 3.76 95.41 -- -- -- 25473 1401 94.95 -- 0.26908 0.26748 0.29815 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 3.764 3.862 -- 71 1483 0.47 0.431 -- 74.25
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 238.985
Anisotropic B[1][1] -14.59
Anisotropic B[1][2] 4.45
Anisotropic B[1][3] -4.59
Anisotropic B[2][2] 2.51
Anisotropic B[2][3] -2.87
Anisotropic B[3][3] 13.15
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.503
r_mcbond_other 13.817
r_gen_planes_other 0.007
r_scbond_other 12.207
r_scangle_other 20.252
r_angle_other_deg 1.609
r_bond_refined_d 0.01
r_bond_other_d 0.008
r_dihedral_angle_4_deg 13.205
r_mcbond_it 13.816
r_mcangle_other 22.104
r_scbond_it 12.207
r_chiral_restr 0.156
r_long_range_B_other 34.492
r_long_range_B_refined 34.492
r_gen_planes_refined 0.007
r_dihedral_angle_2_deg 32.026
r_dihedral_angle_1_deg 4.463
r_mcangle_it 22.106
r_dihedral_angle_3_deg 13.869
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12271
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 4

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing