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Crystal structure of an XXA-pro aminopeptidase from Streptococcus pyogenes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 0.20M ammonium sulfate, 0.10M tri-sodium citrate pH 5.6, 25% w/v PEG4000, cryoprotectant, inclusion of glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.086 α = 90 b = 116.991 β = 96.64 c = 49.447 γ = 90
Symmetry Space Group P 1 21 1
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 210r 2009-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97962 APS 19-BM
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 2 58.52 99.9 0.057 0.057 68.192 8.2 32829 -3
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) 2 2.02 98.3 0.136 0.136 14.9 6.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 58.52 32787 1663 99.85 0.18 0.176 0.1842 0.239 0.2426 RANDOM 19.44
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] 0.59 0.18 -0.17 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.264 r_dihedral_angle_4_deg 15.634 r_dihedral_angle_3_deg 15.189 r_dihedral_angle_1_deg 5.974 r_scangle_it 5.556 r_scbond_it 3.485 r_mcangle_it 2.249 r_angle_refined_deg 1.792 r_mcbond_it 1.275 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.264 r_dihedral_angle_4_deg 15.634 r_dihedral_angle_3_deg 15.189 r_dihedral_angle_1_deg 5.974 r_scangle_it 5.556 r_scbond_it 3.485 r_mcangle_it 2.249 r_angle_refined_deg 1.792 r_mcbond_it 1.275 r_chiral_restr 0.127 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4012 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing RESOLVE model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing