3ZFO

Crystal structure of substrate-like, unprocessed N-terminal protease Npro mutant S169P


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 = 43.33α = 90
b = 41.05β = 98.95
c = 46.25γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2011-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR

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
124398.90.1526.73.910911-3
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)
122.0685.30.553.23.5

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 3ZFN2.0142.841032856599.530.202950.200130.25473RANDOM21.963
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]
1.330.18-0.81-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.91
r_dihedral_angle_4_deg17.841
r_dihedral_angle_3_deg16.735
r_dihedral_angle_1_deg7.44
r_angle_other_deg3.644
r_angle_refined_deg1.826
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_other0.014
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.91
r_dihedral_angle_4_deg17.841
r_dihedral_angle_3_deg16.735
r_dihedral_angle_1_deg7.44
r_angle_other_deg3.644
r_angle_refined_deg1.826
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_other0.014
r_gen_planes_refined0.009
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1175
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing