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Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, complexed with penicillin-V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 5% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.758 α = 90 b = 95.758 β = 90 c = 115.878 γ = 90
Symmetry Space Group P 41 21 2
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 2005-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A
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 1.65 50 94.4 0.057 17.8 5.5 61661
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 1.65 1.71 72.1 0.404
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.65 20 58496 3122 100 0.20686 0.20514 0.23955 0.2297 RANDOM 32.511
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] 0.11 0.11 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.333 r_dihedral_angle_4_deg 17.107 r_dihedral_angle_3_deg 14.571 r_dihedral_angle_1_deg 6.215 r_scangle_it 3.811 r_scbond_it 2.634 r_mcangle_it 1.581 r_angle_refined_deg 1.507 r_mcbond_it 1.032 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.333 r_dihedral_angle_4_deg 17.107 r_dihedral_angle_3_deg 14.571 r_dihedral_angle_1_deg 6.215 r_scangle_it 3.811 r_scbond_it 2.634 r_mcangle_it 1.581 r_angle_refined_deg 1.507 r_mcbond_it 1.032 r_nbtor_refined 0.311 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.195 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3363 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing