X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.25
Temperature 293.0
Details 0.1M Citrate pH 4.25 17.5% PEG6K, ligand soak at pH 6.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.06 α = 90
b = 91.36 β = 103.59
c = 67.55 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
PIXEL DECTRIS PILATUS3 6M mirrors 2016-03-07
Diffraction Radiation
Monochromator Protocol
Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.97624 ESRF ID29

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
1.54 65.66 99.1 0.029 -- 14.6 3.0 -- 77780 -- 2.1 21.7
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)
1.54 1.57 99.0 0.464 -- 2.1 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 1.54 65.66 -- -- -- 73847 3837 98.97 -- 0.17723 0.17574 0.20625 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 1.54 1.58 -- 285 5437 0.255 0.277 -- 99.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.795
Anisotropic B[1][1] 0.04
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.15
Anisotropic B[2][2] 0.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.76
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.295
r_long_range_B_refined 4.922
r_angle_other_deg 1.056
r_gen_planes_other 0.002
r_dihedral_angle_4_deg 20.205
r_mcbond_it 1.458
r_scbond_other 2.295
r_dihedral_angle_2_deg 31.553
r_scangle_other 3.504
r_angle_refined_deg 1.759
r_dihedral_angle_1_deg 4.702
r_mcangle_other 2.162
r_bond_other_d 0.002
r_dihedral_angle_3_deg 14.143
r_long_range_B_other 4.814
r_gen_planes_refined 0.008
r_chiral_restr 0.105
r_mcbond_other 1.453
r_mcangle_it 2.162
r_bond_refined_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3980
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 492

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0131
XDS data reduction
Aimless data scaling
MOLREP phasing