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Crystal structure of Staphylococcus aureus enolase in complex with PEP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 289 0.2M Ammonium acetate, 0.1M Tris pH 8.5, 25%(w/v) Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.74 55.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.154 α = 90 b = 145.154 β = 90 c = 100.512 γ = 90
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 315r 2014-09-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9792 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 100 0.086 40.3 8.2 136548
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 1.63 100 0.467 6.8 8.1
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 5BOF 1.6 50 129690 6858 99.95 0.14923 0.14848 0.1628 0.16356 0.1782 RANDOM 15.677
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] -0.22 -0.22 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.958 r_dihedral_angle_4_deg 15.177 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 6.169 r_long_range_B_refined 4.646 r_long_range_B_other 4.526 r_scangle_other 2.409 r_scbond_it 1.57 r_scbond_other 1.569 r_mcangle_it 1.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.958 r_dihedral_angle_4_deg 15.177 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 6.169 r_long_range_B_refined 4.646 r_long_range_B_other 4.526 r_scangle_other 2.409 r_scbond_it 1.57 r_scbond_other 1.569 r_mcangle_it 1.506 r_mcangle_other 1.506 r_angle_refined_deg 1.376 r_angle_other_deg 1.047 r_mcbond_it 0.945 r_mcbond_other 0.936 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 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 6558 Nucleic Acid Atoms Solvent Atoms 661 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing