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ZnMg substituted aminopeptidase P from E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WL9 PDB ENTRY 1WL9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 ROOM TEMPERATURE HANGING DROP WITH 16% PEG4K, 0.1 M TRIS (PH8.3), 0.2 M MGCL2. CRYOPROTECTED WITH 10-15% MPD., pH 8.30
Crystal Properties Matthews coefficient Solvent content 4.4 68.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.974 α = 90 b = 236.703 β = 106.14 c = 137.637 γ = 90
Symmetry Space Group C 1 2 1
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 MARRESEARCH OSMIC MIRRORS 2004-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200H
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 2.3 29.97 98.9 0.06 17.62 2.8 150167 -3.7 35.89
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 2.3 2.38 97.6 0.32 3.4 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WL9 2.3 29.97 142654 7512 98.9 0.168 0.167 0.197 0.2221 RANDOM 35.06
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] 1.45 0.94 -0.1 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.327 r_dihedral_angle_4_deg 16.933 r_dihedral_angle_3_deg 12.294 r_scangle_it 7.246 r_dihedral_angle_1_deg 5.706 r_scbond_it 5.156 r_mcangle_it 3.238 r_mcbond_it 2.57 r_angle_refined_deg 1.07 r_angle_other_deg 0.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.327 r_dihedral_angle_4_deg 16.933 r_dihedral_angle_3_deg 12.294 r_scangle_it 7.246 r_dihedral_angle_1_deg 5.706 r_scbond_it 5.156 r_mcangle_it 3.238 r_mcbond_it 2.57 r_angle_refined_deg 1.07 r_angle_other_deg 0.763 r_symmetry_vdw_other 0.265 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.197 r_nbd_other 0.172 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.102 r_nbtor_other 0.079 r_chiral_restr 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other 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 Atoms Number Protein Atoms 13964 Nucleic Acid Atoms Solvent Atoms 832 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing