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Crystal Structure of Recombinant Vibrio proteolyticus aminopeptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IQ6 PDB ENTRY 2IQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 VpAP (0.5 mM) in 10 mM Tris buffer, pH 8.0, containing 10 mM KSCN and 400 mM NaCl was equilibrated with 100 mM Tris buffer, pH 8.0, containing 100 mM KSCN and 4.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.397 α = 90 b = 108.397 β = 90 c = 93.529 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2008-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.95 41.89 100 0.135 21 23158 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 100 0.515 31.5 21
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2IQ6 1.95 26.03 17013 21990 1168 95.71 0.19294 0.19115 0.19 0.22776 0.2255 RANDOM 15.414
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.533 r_dihedral_angle_4_deg 15.244 r_dihedral_angle_3_deg 12.788 r_dihedral_angle_1_deg 5.56 r_scangle_it 2.038 r_scbond_it 1.279 r_angle_refined_deg 1.083 r_mcangle_it 0.855 r_mcbond_it 0.454 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.533 r_dihedral_angle_4_deg 15.244 r_dihedral_angle_3_deg 12.788 r_dihedral_angle_1_deg 5.56 r_scangle_it 2.038 r_scbond_it 1.279 r_angle_refined_deg 1.083 r_mcangle_it 0.855 r_mcbond_it 0.454 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.202 r_symmetry_hbond_refined 0.197 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.124 r_metal_ion_refined 0.081 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2235 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 12
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling