3ZFN

Crystal structure of product-like, processed N-terminal protease Npro


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSEMET-SUBSTITUTED PROTEIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5100MM NA ACETATE, PH8.5 50% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.39α = 90
b = 41.16β = 115.38
c = 44.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.54096.50.05153.721445-3
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)
11.51.5495.30.215.23.7

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 DIFFRACTIONMADTHROUGHOUTSEMET-SUBSTITUTED PROTEIN1.528.7120308108596.030.173030.169590.23883RANDOM17.747
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]
1.7-0.78-2.390.73
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.642
r_dihedral_angle_2_deg36.135
r_rigid_bond_restr22.638
r_dihedral_angle_3_deg17.372
r_dihedral_angle_4_deg16.593
r_sphericity_bonded12.638
r_dihedral_angle_1_deg7.414
r_angle_other_deg3.72
r_angle_refined_deg2.111
r_chiral_restr0.165
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free43.642
r_dihedral_angle_2_deg36.135
r_rigid_bond_restr22.638
r_dihedral_angle_3_deg17.372
r_dihedral_angle_4_deg16.593
r_sphericity_bonded12.638
r_dihedral_angle_1_deg7.414
r_angle_other_deg3.72
r_angle_refined_deg2.111
r_chiral_restr0.165
r_gen_planes_other0.022
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1162
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing