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Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Arg
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 6% PEG-8000, 100mM Na Cacodylate pH6.5, 300mM Zn acetate
Crystal Properties Matthews coefficient Solvent content 2.56 52.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.21 α = 90 b = 65.43 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 CCD ADSC QUANTUM 315 2009-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93950 ESRF ID14-4
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 1.6 50 97.8 0.059 20.07 6.02 31676 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 1.7 96.6 0.328 5.4 6.14
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 44.28 30054 1582 100 0.17416 0.17278 0.1731 0.2002 0.1999 RANDOM 17.54
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] 0.82 0.25 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.973 r_dihedral_angle_4_deg 18.554 r_dihedral_angle_3_deg 11.922 r_dihedral_angle_1_deg 5.43 r_scangle_it 3.384 r_scbond_it 2.081 r_angle_refined_deg 1.165 r_mcangle_it 1.093 r_mcbond_it 0.685 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.973 r_dihedral_angle_4_deg 18.554 r_dihedral_angle_3_deg 11.922 r_dihedral_angle_1_deg 5.43 r_scangle_it 3.384 r_scbond_it 2.081 r_angle_refined_deg 1.165 r_mcangle_it 1.093 r_mcbond_it 0.685 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.287 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.204 r_symmetry_hbond_refined 0.18 r_chiral_restr 0.08 r_metal_ion_refined 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 1603 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling FRODO model building PHASER phasing