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Wild-type penicillin-binding protein 5 from E. coli modified by beta-mercaptoethanol
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 5.5 294 24% PEG 4000, 100 mM magnesium acetate, 100 mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.53 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.22 α = 90 b = 50.22 β = 90 c = 138.25 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 2001-07-30 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 2 41.5 99.9 0.065 6.1 2.8 26382 26382 30.37
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 2.07 99.8 0.308 2 2.7 2657
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 THROUGHOUT PDB ENTRY 1HD8 2 14.84 26273 26273 2650 99.9 0.2241 0.2241 0.21926 0.2243 0.26617 0.2659 RANDOM 32.775
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.047 r_dihedral_angle_1_deg 3.506 r_scangle_it 2.723 r_scbond_it 1.659 r_angle_refined_deg 1.332 r_mcangle_it 1.118 r_mcbond_it 0.591 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.218 r_xyhbond_nbd_refined 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.047 r_dihedral_angle_1_deg 3.506 r_scangle_it 2.723 r_scbond_it 1.659 r_angle_refined_deg 1.332 r_mcangle_it 1.118 r_mcbond_it 0.591 r_nbd_refined 0.237 r_symmetry_vdw_refined 0.218 r_xyhbond_nbd_refined 0.207 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.095 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2681 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling