6MEN

Crystal structure of a Tylonycteris bat coronavirus HKU4 macrodomain in complex with adenosine diphosphate glucose (ADP-glucose)


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 295.0
Details 20-25% PEG3350, 0.1 M HEPES, pH 7.0-7.5, protein:ligand molar ratio 1:10

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 33.55 α = 73.04
b = 41.69 β = 88.37
c = 60 γ = 88.05
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300-HS Mirrors 2017-07-02
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID

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
1.5 39.86 99.9 0.129 -- -- 7.5 -- 49739 -- -- 16.1
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)
1.5 1.53 100.0 1.284 -- 1.9 7.4 --

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 1.5 29.21 -- 0.0 -- 47290 2447 99.9 -- 0.1747 0.1729 0.2086 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 1.5 1.539 -- 168 3527 0.259 0.323 0.0 99.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.8
Anisotropic B[1][1] -0.2
Anisotropic B[1][2] -0.13
Anisotropic B[1][3] -0.02
Anisotropic B[2][2] 0.18
Anisotropic B[2][3] -0.01
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.11
r_dihedral_angle_2_deg 39.112
r_sphericity_bonded 18.792
r_angle_other_deg 0.908
r_dihedral_angle_3_deg 11.359
r_angle_refined_deg 1.683
r_rigid_bond_restr 1.336
r_bond_refined_d 0.006
r_dihedral_angle_1_deg 6.728
r_dihedral_angle_4_deg 15.052
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2426
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 237

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0222
Aimless data scaling version: 0.5.32
PDB_EXTRACT data extraction version: 3.24
XDS data reduction version: Version Nov. 1, 2016
PHASER phasing version: 2.8.2