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2.3 Angstrom Crystal Structure of the Monomeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 Protein: 13.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 5mM Penicillin V;
Screen: Classics II (H7), 0.15M DL-Malic acid (pH 7.0), 20% (w/v) PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.44 α = 90 b = 64.34 β = 90 c = 182.786 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2015-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 29.12 99.8 0.131 0.131 22.4 7 33135 -3 38.2
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 2.3 2.34 100 0.637 3.3 7.2
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 5DVY 2.3 29.12 30970 1677 98.77 0.19925 0.19676 0.2053 0.24445 0.2497 RANDOM 45.23
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] -1.47 -3.71 5.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.115 r_dihedral_angle_3_deg 10.362 r_dihedral_angle_4_deg 8.619 r_long_range_B_refined 7.351 r_long_range_B_other 7.34 r_scangle_other 4.822 r_mcangle_it 4.153 r_mcangle_other 4.153 r_scbond_it 3.013 r_scbond_other 3.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.115 r_dihedral_angle_3_deg 10.362 r_dihedral_angle_4_deg 8.619 r_long_range_B_refined 7.351 r_long_range_B_other 7.34 r_scangle_other 4.822 r_mcangle_it 4.153 r_mcangle_other 4.153 r_scbond_it 3.013 r_scbond_other 3.012 r_dihedral_angle_1_deg 2.825 r_mcbond_other 2.617 r_mcbond_it 2.616 r_angle_refined_deg 1.517 r_angle_other_deg 0.751 r_chiral_restr 0.09 r_gen_planes_refined 0.022 r_gen_planes_other 0.019 r_bond_refined_d 0.011 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4898 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing