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Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with tripeptide Met-Ala-Ser
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, 350mM Zn acetate
Crystal Properties Matthews coefficient Solvent content 2.58 52.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.15 α = 90 b = 65.55 β = 90 c = 88.84 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 4r 2008-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.7 50 98.4 0.087 15.88 7.24 26908 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 1.7 1.8 96.9 0.475 4.45 7.28
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 1.7 44.41 25415 1338 98.5 0.15 0.149 0.1588 0.188 0.2004 RANDOM 16.81
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] 0.32 0.84 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.228 r_dihedral_angle_4_deg 20.932 r_dihedral_angle_3_deg 11.634 r_long_range_B_refined 7.72 r_long_range_B_other 6.793 r_dihedral_angle_1_deg 6.52 r_scangle_other 3.101 r_angle_refined_deg 2.514 r_scbond_it 2.042 r_scbond_other 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.228 r_dihedral_angle_4_deg 20.932 r_dihedral_angle_3_deg 11.634 r_long_range_B_refined 7.72 r_long_range_B_other 6.793 r_dihedral_angle_1_deg 6.52 r_scangle_other 3.101 r_angle_refined_deg 2.514 r_scbond_it 2.042 r_scbond_other 2.04 r_mcangle_other 1.542 r_mcangle_it 1.535 r_angle_other_deg 1.231 r_mcbond_it 1.057 r_mcbond_other 1.039 r_chiral_restr 0.38 r_bond_refined_d 0.033 r_gen_planes_refined 0.016 r_bond_other_d 0.003 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 1600 Nucleic Acid Atoms Solvent Atoms 367 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling FRODO model building PHASER phasing