2BX3

Crystal Structure of SARS Coronavirus Main Proteinase (P43212)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UJ1PDB ENTRY 1UJ1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.915% PEG6000, 0.1M MES PH 5.9, 3% MPD
Crystal Properties
Matthews coefficientSolvent content
1.830

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.675α = 90
b = 69.675β = 90
c = 100.197γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2004-11-11MSINGLE 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
1240.821000.1520.615.617333220.32
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)
122.1199.80.564.913.9

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 1UJ1256.81639588499.90.180.1750.257RANDOM20.36
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]
-1.77-1.773.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.603
r_dihedral_angle_4_deg21.846
r_dihedral_angle_3_deg16.821
r_dihedral_angle_1_deg9.207
r_mcangle_it2.183
r_scangle_it1.925
r_angle_refined_deg1.718
r_mcbond_it1.709
r_scbond_it1.347
r_angle_other_deg0.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.603
r_dihedral_angle_4_deg21.846
r_dihedral_angle_3_deg16.821
r_dihedral_angle_1_deg9.207
r_mcangle_it2.183
r_scangle_it1.925
r_angle_refined_deg1.718
r_mcbond_it1.709
r_scbond_it1.347
r_angle_other_deg0.818
r_symmetry_hbond_refined0.307
r_symmetry_vdw_refined0.3
r_xyhbond_nbd_refined0.29
r_symmetry_vdw_other0.267
r_nbd_refined0.229
r_nbd_other0.209
r_nbtor_refined0.197
r_chiral_restr0.117
r_nbtor_other0.099
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms2326
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing