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Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with inhibitor AT020
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 8% PEG-8000, 100mM imidazole pH7.5, 400mM Zn acetate
Crystal Properties Matthews coefficient Solvent content 2.59 52.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41 α = 90 b = 65.27 β = 90 c = 88.47 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 1.8 50 99.7 0.148 0.994 8.84 6.39 22777 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 1.8 1.9 98.6 0.924 1.68 6.24
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 1.8 44.24 21535 1134 100 0.18644 0.18423 0.1891 0.2292 0.2332 RANDOM 19.829
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] -0.07 0.97 -0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 21.435 r_dihedral_angle_3_deg 12.397 r_dihedral_angle_1_deg 5.964 r_scangle_it 3.783 r_scbond_it 2.478 r_angle_refined_deg 1.414 r_mcangle_it 1.361 r_mcbond_it 0.876 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 21.435 r_dihedral_angle_3_deg 12.397 r_dihedral_angle_1_deg 5.964 r_scangle_it 3.783 r_scbond_it 2.478 r_angle_refined_deg 1.414 r_mcangle_it 1.361 r_mcbond_it 0.876 r_nbtor_refined 0.299 r_xyhbond_nbd_refined 0.225 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.184 r_metal_ion_refined 0.161 r_chiral_restr 0.097 r_symmetry_metal_ion_refined 0.063 r_bond_refined_d 0.015 r_gen_planes_refined 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_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 1573 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing FRODO model building