☰ Navigation Tabs
CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 IN COMPLEX WITH DEACYLATED PRODUCT OF CEFOPERAZONE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 294 1.26 M (NH4)2SO4; 0.1 M CHES pH 9.5; 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.33 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.884 α = 90 b = 41.264 β = 117.42 c = 87.786 γ = 90
Symmetry Space Group C 1 2 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 315 2011-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97960 Diamond I02
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 2.7 30 100 0.092 14.5 3.7 15866
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 2.7 2.8 100 0.722 1.9 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 5DF8 2.7 29.97 15029 786 99.58 0.2046 0.20236 0.2031 0.24927 0.2464 RANDOM 75.155
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] -4.43 1.75 -3.26 4.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.469 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_4_deg 11.152 r_long_range_B_refined 8.339 r_long_range_B_other 8.337 r_scangle_other 5.892 r_dihedral_angle_1_deg 4.858 r_mcangle_it 4.667 r_mcangle_other 4.667 r_scbond_it 3.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.469 r_dihedral_angle_3_deg 12.857 r_dihedral_angle_4_deg 11.152 r_long_range_B_refined 8.339 r_long_range_B_other 8.337 r_scangle_other 5.892 r_dihedral_angle_1_deg 4.858 r_mcangle_it 4.667 r_mcangle_other 4.667 r_scbond_it 3.664 r_scbond_other 3.662 r_mcbond_it 2.987 r_mcbond_other 2.978 r_angle_refined_deg 0.903 r_angle_other_deg 0.669 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3886 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing