2VRI

Structure of the NSP3 X-domain of human coronavirus NL63


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.244.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.97α = 90
b = 54.77β = 90
c = 57.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.740990.18.75.5199142
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)
11.71.7488.30.951.644.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2ACF1.939.591289299099.80.1890.1850.243RANDOM21.25
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]
0.931.34-2.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.082
r_dihedral_angle_3_deg13.902
r_dihedral_angle_4_deg13.357
r_dihedral_angle_1_deg7.453
r_scangle_it3.906
r_scbond_it2.532
r_mcangle_it1.604
r_angle_refined_deg1.52
r_mcbond_it0.935
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.082
r_dihedral_angle_3_deg13.902
r_dihedral_angle_4_deg13.357
r_dihedral_angle_1_deg7.453
r_scangle_it3.906
r_scbond_it2.532
r_mcangle_it1.604
r_angle_refined_deg1.52
r_mcbond_it0.935
r_nbtor_refined0.315
r_symmetry_vdw_refined0.262
r_nbd_refined0.22
r_symmetry_hbond_refined0.159
r_xyhbond_nbd_refined0.138
r_chiral_restr0.103
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1320
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
HKLdata reduction
SCALEPACKdata scaling
PHASERphasing