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Asp260Ala Escherichia coli Aminopeptidase P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BHC PDB ENTRY 2BHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 10 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 30% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH AND 1 MM MNCL2 FOR 1 HR AT 4C PRIOR TO CRYOCOOLING.
Crystal Properties Matthews coefficient Solvent content 5.5 77.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.588 α = 90 b = 137.588 β = 90 c = 231.948 γ = 90
Symmetry Space Group I 41 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 CCD MARRESEARCH 2005-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.9 24.13 91.7 0.1 10.5 3.8 22735 6 76.6
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 2.9 3.06 94.5 0.53 2 3.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BHC 2.9 23.89 21640 1091 91 0.171 0.169 0.1803 0.202 0.2109 RANDOM 66.25
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] 2.98 2.98 -5.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.241 r_dihedral_angle_4_deg 14.321 r_dihedral_angle_3_deg 12.831 r_dihedral_angle_1_deg 5.628 r_scangle_it 1.907 r_scbond_it 1.14 r_angle_refined_deg 1.074 r_mcangle_it 0.811 r_angle_other_deg 0.72 r_mcbond_it 0.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.241 r_dihedral_angle_4_deg 14.321 r_dihedral_angle_3_deg 12.831 r_dihedral_angle_1_deg 5.628 r_scangle_it 1.907 r_scbond_it 1.14 r_angle_refined_deg 1.074 r_mcangle_it 0.811 r_angle_other_deg 0.72 r_mcbond_it 0.504 r_symmetry_vdw_other 0.215 r_nbd_refined 0.201 r_nbtor_refined 0.175 r_nbd_other 0.163 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.122 r_symmetry_vdw_refined 0.122 r_nbtor_other 0.078 r_chiral_restr 0.06 r_bond_refined_d 0.008 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 3484 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling