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Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in apo state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NZO model constructed by Modeller using 1NZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 292 PEG 8000, pH 4.5, vapor diffusion, hanging drop, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.77 55.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.949 α = 90 b = 184.853 β = 100.62 c = 81.61 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 Q315R MIRRORS 2008-05-03 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 2.1 50 97.7 0.062 12.3 2.5 93487
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) 2.1 2.18 97 0.481 2.3
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 model constructed by Modeller using 1NZO 2.1 50 93444 4673 97.2 0.21 0.207 0.2006 0.259 0.2494 RANDOM 40.19
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] 2.15 0.09 -2.1 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.408 r_dihedral_angle_3_deg 22.503 r_dihedral_angle_4_deg 20.196 r_dihedral_angle_1_deg 13.226 r_scangle_it 6.547 r_scbond_it 4.234 r_mcangle_it 2.762 r_mcbond_it 1.595 r_angle_refined_deg 0.858 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.408 r_dihedral_angle_3_deg 22.503 r_dihedral_angle_4_deg 20.196 r_dihedral_angle_1_deg 13.226 r_scangle_it 6.547 r_scbond_it 4.234 r_mcangle_it 2.762 r_mcbond_it 1.595 r_angle_refined_deg 0.858 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 10637 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 86
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection PHASER phasing