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Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT019
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, 400mM Zn acetate
Crystal Properties Matthews coefficient Solvent content 2.61 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.15 α = 90 b = 65.71 β = 90 c = 88.54 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 2.4 50 99.9 0.183 0.987 8.88 5.49 18118 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 2.4 2.46 99.9 0.783 3.15 5.09
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 2.4 44.28 9374 494 100 0.16517 0.16198 0.172 0.22517 0.2312 RANDOM 21.215
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] -0.57 0.6 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_4_deg 22.316 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_1_deg 6.965 r_scangle_it 4.972 r_scbond_it 3.067 r_angle_refined_deg 1.875 r_mcangle_it 1.762 r_mcbond_it 1.019 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.389 r_dihedral_angle_4_deg 22.316 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_1_deg 6.965 r_scangle_it 4.972 r_scbond_it 3.067 r_angle_refined_deg 1.875 r_mcangle_it 1.762 r_mcbond_it 1.019 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.303 r_xyhbond_nbd_refined 0.257 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.196 r_metal_ion_refined 0.175 r_chiral_restr 0.119 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 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_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 1581 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling FRODO model building PHASER phasing