3ZFR

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5100MM NAACETATE, PH 8.5 50% PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.77α = 90
b = 41.07β = 114.6
c = 43.56γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2011-06-19MSINGLE 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
11.820.598.70.0710.83.512457-3
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)
11.81.991.30.6223.3

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 3ZFN1.820.541180163299.150.181990.179590.22836RANDOM23.102
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]
0.57-1.05-0.250.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.197
r_dihedral_angle_4_deg19.62
r_dihedral_angle_3_deg16.927
r_dihedral_angle_1_deg7.86
r_angle_other_deg3.672
r_angle_refined_deg1.987
r_chiral_restr0.121
r_gen_planes_other0.026
r_bond_refined_d0.019
r_gen_planes_refined0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.197
r_dihedral_angle_4_deg19.62
r_dihedral_angle_3_deg16.927
r_dihedral_angle_1_deg7.86
r_angle_other_deg3.672
r_angle_refined_deg1.987
r_chiral_restr0.121
r_gen_planes_other0.026
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1162
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing