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Ca-substituted form of E. coli aminopeptidase P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M35 PDB ENTRY 1M35
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 25% PEG 4K, 0.1 MM EDTA, 0.1 M TRIS (PH 8.2), 0.2 M NA ACETATE CRYSTALS SOAKED IN 30% ISOPROPANOL PLUS 5 MM CACL2 FOR 10 MIN PRIOR TO FREEZING
Crystal Properties Matthews coefficient Solvent content 4.4 71.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.359 α = 90 b = 312.688 β = 90 c = 160.198 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 113 IMAGE PLATE RIGAKU RAXIS IIC YALE MIRRORS 1999-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 H
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 2.4 30 94.5 0.04 19.6 2.1 192310 -3 40.59
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 2.4 2.48 86 0.16 4.5 1.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1M35 2.4 182.57 182590 9688 94.8 0.176 0.175 0.1808 0.2 0.2028 RANDOM 26.12
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] -0.58 -0.67 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.867 r_scangle_it 3.097 r_scbond_it 1.753 r_angle_refined_deg 1.254 r_mcangle_it 1.077 r_angle_other_deg 0.833 r_mcbond_it 0.529 r_symmetry_vdw_other 0.295 r_nbd_other 0.235 r_nbd_refined 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.867 r_scangle_it 3.097 r_scbond_it 1.753 r_angle_refined_deg 1.254 r_mcangle_it 1.077 r_angle_other_deg 0.833 r_mcbond_it 0.529 r_symmetry_vdw_other 0.295 r_nbd_other 0.235 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.176 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.086 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_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 20931 Nucleic Acid Atoms Solvent Atoms 1072 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling