X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.15
Details 0.1 M MES pH 6.5, 12% PEG 20000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.81 α = 90
b = 56.94 β = 104.86
c = 60.69 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2017-11-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.980 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
1.6 46.22 98.86 -- -- -- 6.7 -- 41326 -- -- 23.74
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)
1.6 1.657 99.9 -- -- 1.32 7.0 --

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 1.6 46.22 -- -- -- 39198 2021 98.88 -- 0.17122 0.16955 0.20333 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 1.6 1.642 -- 158 2895 0.629 0.676 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.148
Anisotropic B[1][1] -0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.35
Anisotropic B[2][2] -0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.12
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 1.638
r_angle_refined_deg 2.53
r_long_range_B_refined 6.377
r_angle_other_deg 1.287
r_scangle_other 4.544
r_gen_planes_other 0.002
r_scbond_it 3.047
r_bond_other_d 0.003
r_gen_planes_refined 0.014
r_mcbond_it 1.64
r_long_range_B_other 6.376
r_dihedral_angle_4_deg 14.026
r_scbond_other 3.046
r_mcangle_other 2.3
r_mcangle_it 2.301
r_bond_refined_d 0.03
r_dihedral_angle_1_deg 6.224
r_dihedral_angle_2_deg 35.692
r_chiral_restr 0.19
r_dihedral_angle_3_deg 14.169
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2543
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 423

Software

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