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Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with actinonin
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 9% PEG-8000, 100mM Na Cacodylate pH6.5, 400mM Zn acetate
Crystal Properties Matthews coefficient Solvent content 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.84 α = 90 b = 66.16 β = 90 c = 88.86 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 1.99 50 98.8 0.111 14.14 6.97 17013 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 1.99 2.11 93.4 0.408 5.62 6.94
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 44.41 16023 844 99.82 0.1536 0.15117 0.1598 0.19805 0.2011 RANDOM 19.648
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] 0.16 0.49 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.3 r_dihedral_angle_4_deg 19.885 r_dihedral_angle_3_deg 13.085 r_dihedral_angle_1_deg 6.847 r_long_range_B_refined 6.398 r_long_range_B_other 6.004 r_scangle_other 3.496 r_angle_refined_deg 2.393 r_scbond_it 2.254 r_scbond_other 2.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.3 r_dihedral_angle_4_deg 19.885 r_dihedral_angle_3_deg 13.085 r_dihedral_angle_1_deg 6.847 r_long_range_B_refined 6.398 r_long_range_B_other 6.004 r_scangle_other 3.496 r_angle_refined_deg 2.393 r_scbond_it 2.254 r_scbond_other 2.253 r_mcangle_other 1.719 r_mcangle_it 1.715 r_angle_other_deg 1.306 r_mcbond_it 1.164 r_mcbond_other 1.116 r_chiral_restr 0.365 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 r_bond_other_d 0.002 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 1569 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling FRODO model building PHASER phasing