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Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EX2 PDB ENTRY 2EX2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES pH 7.5, 25% (w/v) PEG 6000, 5% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.548 α = 90 b = 92.59 β = 107.75 c = 104.882 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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 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 1.6 20 94.9 0.062 4 146613
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 1.6 1.66 84.9 0.26
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 PDB ENTRY 2EX2 1.6 19.98 139255 7346 100 0.17253 0.17089 0.1646 0.20408 0.1968 RANDOM 20.209
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] -0.35 -0.12 0.15 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.179 r_dihedral_angle_4_deg 23.155 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_1_deg 6.213 r_scangle_it 6.196 r_scbond_it 3.943 r_angle_refined_deg 2.547 r_mcangle_it 2.526 r_mcbond_it 1.531 r_chiral_restr 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.179 r_dihedral_angle_4_deg 23.155 r_dihedral_angle_3_deg 13.636 r_dihedral_angle_1_deg 6.213 r_scangle_it 6.196 r_scbond_it 3.943 r_angle_refined_deg 2.547 r_mcangle_it 2.526 r_mcbond_it 1.531 r_chiral_restr 0.2 r_bond_refined_d 0.031 r_gen_planes_refined 0.015 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 7012 Nucleic Acid Atoms Solvent Atoms 924 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing