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Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor SMP289
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 13% PEG-8000, 100mM Imidazole pH6.5, 400mM Zn acetate
Crystal Properties Matthews coefficient Solvent content 2.67 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.47 α = 90 b = 65.97 β = 90 c = 89.32 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 2010-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.09 50 94.8 0.093 12.04 3.2 26386 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.22 86.3 0.322 0.381 3.99 3.16
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 2AIE 2.1 44.66 14121 744 99.9 0.1568 0.1539 0.1614 0.2112 0.2079 RANDOM 22.14
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] 0.49 0.68 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.28 r_dihedral_angle_4_deg 20.749 r_dihedral_angle_3_deg 14.373 r_long_range_B_refined 6.987 r_dihedral_angle_1_deg 6.708 r_long_range_B_other 6.54 r_scangle_other 4.083 r_scbond_it 2.604 r_scbond_other 2.603 r_angle_refined_deg 2.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.28 r_dihedral_angle_4_deg 20.749 r_dihedral_angle_3_deg 14.373 r_long_range_B_refined 6.987 r_dihedral_angle_1_deg 6.708 r_long_range_B_other 6.54 r_scangle_other 4.083 r_scbond_it 2.604 r_scbond_other 2.603 r_angle_refined_deg 2.311 r_mcangle_it 2.231 r_mcangle_other 2.23 r_mcbond_it 1.45 r_mcbond_other 1.411 r_angle_other_deg 1.191 r_chiral_restr 0.329 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1575 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling FRODO model building PHASER phasing