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Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethyl ketone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HXE PDB ENTRY 4HXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 2.5 M 1,6-hexanediol, 0.20 M MgCl2, 0.1 M Tris/HCl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.21 61.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.057 α = 90 b = 184.057 β = 90 c = 145.529 γ = 120
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 IV++ confocal mirrors 2010-11-15 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 1.6 20 99.2 0.066 22.25 7.03 122438 122438 -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 1.6 1.64 94.4 0.738 2.57 5.24
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 4HXE 1.601 19.74 116219 116219 6218 99.22 0.15617 0.15457 0.166 0.186 0.1958 RANDOM 19.811
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] 0.05 0.03 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.562 r_dihedral_angle_4_deg 18.017 r_dihedral_angle_3_deg 13.597 r_dihedral_angle_1_deg 7.019 r_angle_refined_deg 2.248 r_angle_other_deg 1.108 r_chiral_restr 0.144 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.562 r_dihedral_angle_4_deg 18.017 r_dihedral_angle_3_deg 13.597 r_dihedral_angle_1_deg 7.019 r_angle_refined_deg 2.248 r_angle_other_deg 1.108 r_chiral_restr 0.144 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5019 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 102
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling