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Binding of inhibitors by Acylaminoacyl peptidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VE6 PDB ENTRY 1VE6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 78mM sodium acetate, 0.44mM EDTA, 2.2% PEG 4000, 0.56% beta-octyl-glucoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.682 α = 90 b = 103.989 β = 90 c = 168.594 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IIC 2005-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2 19.537 94.8 0.115 13.07 76464 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 80.2 0.383 3.1 8216
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 (All) 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 1VE6 2.01 19.52 68079 68079 3602 94.75 0.17761 0.17761 0.17554 0.186 0.21693 0.2245 RANDOM (AS FOR RELATED PDB ENTRY 2HU5) 17.854
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] -0.07 -0.06 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.421 r_scangle_it 1.968 r_mcangle_it 1.747 r_angle_refined_deg 1.274 r_scbond_it 1.21 r_mcbond_it 1.087 r_angle_other_deg 0.838 r_symmetry_vdw_refined 0.266 r_nbd_other 0.248 r_symmetry_vdw_other 0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.421 r_scangle_it 1.968 r_mcangle_it 1.747 r_angle_refined_deg 1.274 r_scbond_it 1.21 r_mcbond_it 1.087 r_angle_other_deg 0.838 r_symmetry_vdw_refined 0.266 r_nbd_other 0.248 r_symmetry_vdw_other 0.248 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.086 r_nbtor_other 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 8623 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing