3ZFP

Crystal structure of product-like, processed N-terminal protease Npro with internal His-Tag


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZFNPDB ENTRY 3ZFN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5100MM NAACETATE, PH 8.5 25% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.39α = 90
b = 41.04β = 115.31
c = 44.51γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
11.2520.598.90.0512.43.737962-3
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)
11.251.3297.40.492.63.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3ZFN1.2521.1736027192798.870.160820.158390.20662RANDOM15.167
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]
0.33-2.10.180.33
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free56.89
r_dihedral_angle_2_deg37.341
r_sphericity_bonded23.493
r_rigid_bond_restr23.435
r_dihedral_angle_3_deg15.196
r_dihedral_angle_4_deg8.889
r_dihedral_angle_1_deg7.814
r_angle_other_deg3.719
r_angle_refined_deg2.604
r_chiral_restr0.153
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free56.89
r_dihedral_angle_2_deg37.341
r_sphericity_bonded23.493
r_rigid_bond_restr23.435
r_dihedral_angle_3_deg15.196
r_dihedral_angle_4_deg8.889
r_dihedral_angle_1_deg7.814
r_angle_other_deg3.719
r_angle_refined_deg2.604
r_chiral_restr0.153
r_gen_planes_other0.03
r_bond_refined_d0.026
r_gen_planes_refined0.014
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 Atoms1171
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing