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Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 1.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HD8 PDB ENTRY 1HD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20% PEG 4000, 100 mM Tris pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.2 α = 90 b = 50.2 β = 90 c = 135.76 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV mirrors 2002-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.9 36.6 98.7 0.073 7.1 6 29772 25.9
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) 1.9 1.97 88.4 0.354 1.8 3.4 3024
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Refinement from a lower resolution structure THROUGHOUT PDB ENTRY 1HD8 1.9 15 29705 29705 1507 98.7 0.2091 0.20913 0.20727 0.2132 0.24454 0.2457 RANDOM 29.263
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] -0.34 -0.17 -0.34 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.483 r_dihedral_angle_1_deg 3.332 r_scangle_it 2.757 r_scbond_it 1.633 r_angle_refined_deg 1.212 r_mcangle_it 1.187 r_mcbond_it 0.62 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.483 r_dihedral_angle_1_deg 3.332 r_scangle_it 2.757 r_scbond_it 1.633 r_angle_refined_deg 1.212 r_mcangle_it 1.187 r_mcbond_it 0.62 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.085 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2649 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction d*TREK data scaling