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Aminopeptidase S from S. aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other authors' current, unpublished structure of a thermophilic homologue of AmpS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 292 HEPES/NaOH, ammonium sulfate, PEG 6K, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.33 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.181 α = 90 b = 81.858 β = 90 c = 152.885 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 100 CCD MARRESEARCH 2004-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 20 98.2 0.064 0.064 26 5 40684 40684 21.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 96.9 0.396 0.396 2.3 5 1905
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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(DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT authors' current, unpublished structure of a thermophilic homologue of AmpS 1.8 20 40678 40678 2034 98.84 0.17202 0.17202 0.16998 0.21154 0.2176 RANDOM 20.969
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] 0.63 1.28 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.381 r_scangle_it 5.623 r_angle_other_deg 3.784 r_scbond_it 3.451 r_mcangle_it 2.05 r_angle_refined_deg 1.756 r_mcbond_it 1.134 r_symmetry_vdw_other 0.304 r_nbd_other 0.284 r_nbd_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.381 r_scangle_it 5.623 r_angle_other_deg 3.784 r_scbond_it 3.451 r_mcangle_it 2.05 r_angle_refined_deg 1.756 r_mcbond_it 1.134 r_symmetry_vdw_other 0.304 r_nbd_other 0.284 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.2 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.116 r_nbtor_other 0.107 r_metal_ion_refined 0.055 r_bond_refined_d 0.02 r_gen_planes_other 0.013 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3296 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing