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Crystal structure of Aminopeptidase N in complex with phosphonic acid analogue of homophenylalanine L-(R)-hPheP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 2.0 M Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.83 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 224.047 α = 90 b = 224.047 β = 90 c = 57.807 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 CCD ADSC QUANTUM 315r mirrors 2013-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.85 29.86 100 0.086 17 91950 91950 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 2GTQ 1.85 29.86 2 2 87639 83245 4394 95.05 0.1578 0.1559 0.19298 0.2012 RANDOM 24.925
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] 0.29 0.29 0.29 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.196 r_dihedral_angle_4_deg 19.831 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 6.096 r_angle_refined_deg 1.936 r_angle_other_deg 0.925 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.196 r_dihedral_angle_4_deg 19.831 r_dihedral_angle_3_deg 13.987 r_dihedral_angle_1_deg 6.096 r_angle_refined_deg 1.936 r_angle_other_deg 0.925 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 6852 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 71
Software Software Software Name Purpose SBC-Collect data collection CCP4 model building MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling CCP4 phasing