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His354Ala Escherichia coli Aminopeptidase P
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 8.5 277 HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 10 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 32 % PEG 4K, 0.1 M TRIS PH 8.5. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD AND 1 MM MNCL2 FOR 30 MIN AT 4C PRIOR TO CRYOCOOLING.
Crystal Properties Matthews coefficient Solvent content 4.4 71.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.252 α = 90 b = 177.252 β = 90 c = 96.77 γ = 120
Symmetry Space Group P 64 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 100 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2005-03-02 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 1.7 76.7 100 0.07 16.5 5.9 97989 6 21.17
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 1.7 1.79 100 0.67 1.9 5.1
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 1WL9 1.7 154.3 94990 2965 100 0.159 0.158 0.1721 0.176 0.1874 RANDOM 18.59
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] 0.12 0.06 0.12 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.339 r_dihedral_angle_4_deg 14.078 r_dihedral_angle_3_deg 10.781 r_dihedral_angle_1_deg 5.997 r_scangle_it 5.662 r_scbond_it 3.855 r_mcangle_it 2.29 r_mcbond_it 2.065 r_angle_refined_deg 1.183 r_angle_other_deg 0.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.339 r_dihedral_angle_4_deg 14.078 r_dihedral_angle_3_deg 10.781 r_dihedral_angle_1_deg 5.997 r_scangle_it 5.662 r_scbond_it 3.855 r_mcangle_it 2.29 r_mcbond_it 2.065 r_angle_refined_deg 1.183 r_angle_other_deg 0.792 r_symmetry_vdw_other 0.3 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.206 r_nbd_other 0.177 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.125 r_nbtor_other 0.079 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 3501 Nucleic Acid Atoms Solvent Atoms 636 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling