5HOL

The crystal structure of the MERS-CoV macro domain with ADP-ribose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FAV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1 M Bis-Tris propane pH 7.0, 1.3 M sodium citrate tribasic dihydrate.
Crystal Properties
Matthews coefficientSolvent content
2.6453.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.3α = 90
b = 66.53β = 90
c = 89.5γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.992PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5953.391000.04727.610.924489
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.681000.2119.210.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2FAV1.5953.3924489131599.990.142190.140920.16534RANDOM20.767
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-1.191.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.781
r_dihedral_angle_4_deg18.385
r_dihedral_angle_3_deg12.511
r_long_range_B_refined7.982
r_long_range_B_other7.607
r_dihedral_angle_1_deg6.693
r_scangle_other5.194
r_scbond_it3.701
r_scbond_other3.698
r_mcangle_other3.346
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.781
r_dihedral_angle_4_deg18.385
r_dihedral_angle_3_deg12.511
r_long_range_B_refined7.982
r_long_range_B_other7.607
r_dihedral_angle_1_deg6.693
r_scangle_other5.194
r_scbond_it3.701
r_scbond_other3.698
r_mcangle_other3.346
r_mcangle_it3.344
r_angle_refined_deg2.487
r_mcbond_it2.282
r_mcbond_other2.268
r_angle_other_deg1.187
r_chiral_restr0.155
r_bond_refined_d0.027
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1242
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing