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Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT018
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 7.5 293 7% PEG-8000, 100mM imidazole pH7.5, 300mM Zn acetate
Crystal Properties Matthews coefficient Solvent content 2.61 52.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.07 α = 90 b = 65.49 β = 90 c = 88.79 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 PIXEL DECTRIS PILATUS3 6M 2014-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97918 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 50 99.6 0.095 0.996 9.13 3.79 60836 2 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 1.6 1.64 99 0.896 1.72 3.66
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 1.6 44.41 30677 1615 100 0.18723 0.18583 0.1996 0.21406 0.2239 RANDOM 16.86
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] 0.13 0.53 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.6 r_dihedral_angle_4_deg 18.318 r_dihedral_angle_3_deg 11.105 r_dihedral_angle_1_deg 5.397 r_scangle_it 3.731 r_scbond_it 2.362 r_angle_refined_deg 1.357 r_mcangle_it 1.3 r_mcbond_it 0.818 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.6 r_dihedral_angle_4_deg 18.318 r_dihedral_angle_3_deg 11.105 r_dihedral_angle_1_deg 5.397 r_scangle_it 3.731 r_scbond_it 2.362 r_angle_refined_deg 1.357 r_mcangle_it 1.3 r_mcbond_it 0.818 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.242 r_xyhbond_nbd_refined 0.206 r_nbd_refined 0.203 r_metal_ion_refined 0.17 r_symmetry_hbond_refined 0.103 r_chiral_restr 0.086 r_symmetry_metal_ion_refined 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_other r_symmetry_vdw_other r_symmetry_hbond_other 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 1577 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling FRODO model building PHASER phasing