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Crystal structure of PBP1a from drug-resistant strain 5204 from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CW6 PDB ENTRY 2CW6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 0.1M MES PH6, 21% PEG6000, 17MM BACL2
Crystal Properties Matthews coefficient Solvent content 2.3 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.96 α = 90 b = 67.03 β = 100.89 c = 49.13 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD ADSC CCD 2005-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 19.7 96.1 0.12 11.1 3.77 29802 18.23
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 1.9 2.06 93.2 0.37 4 3.86
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2CW6 1.9 19.74 27167 3026 100 0.213 0.21 0.246 RANDOM 13.11
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] -0.27 -0.42 0.42 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.504 r_dihedral_angle_4_deg 15.711 r_dihedral_angle_3_deg 10.65 r_scangle_it 2.843 r_scbond_it 2.058 r_dihedral_angle_1_deg 1.958 r_mcangle_it 1.943 r_angle_refined_deg 1.465 r_mcbond_it 1.238 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.504 r_dihedral_angle_4_deg 15.711 r_dihedral_angle_3_deg 10.65 r_scangle_it 2.843 r_scbond_it 2.058 r_dihedral_angle_1_deg 1.958 r_mcangle_it 1.943 r_angle_refined_deg 1.465 r_mcbond_it 1.238 r_nbtor_refined 0.321 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.225 r_chiral_restr 0.161 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.136 r_gen_planes_refined 0.007 r_bond_refined_d 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2985 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing