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Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in complex with a substrate fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IT9 apo PBP6 model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 292 PEG 8000, pH 4.5, vapor diffusion, hanging drop, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.81 56.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.534 α = 90 b = 185.351 β = 100.99 c = 82.329 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 2009-04-10 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 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 1.8 50 88 0.07 16.5 2.2 136723
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 1.8 1.86 84 0.59 2.2 12997
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 apo PBP6 model 1.8 40.2 136655 6831 87.84 0.207 0.205 0.2034 0.254 0.2488 RANDOM 38.923
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] 2.8 0.27 -2.87 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.959 r_dihedral_angle_3_deg 19.198 r_dihedral_angle_4_deg 18.584 r_dihedral_angle_1_deg 14.318 r_scangle_it 8.051 r_scbond_it 5.261 r_mcangle_it 3.512 r_mcbond_it 2.29 r_angle_refined_deg 1.733 r_chiral_restr 0.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.959 r_dihedral_angle_3_deg 19.198 r_dihedral_angle_4_deg 18.584 r_dihedral_angle_1_deg 14.318 r_scangle_it 8.051 r_scbond_it 5.261 r_mcangle_it 3.512 r_mcbond_it 2.29 r_angle_refined_deg 1.733 r_chiral_restr 0.178 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10613 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 53
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing