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The crystal structure of a hemolysin domain from Enterococcus faecalis V583
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 15% Ethanol, 0.1M MES, 0.2M Zn(OAC)2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.12 41.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.494 α = 90 b = 39.494 β = 90 c = 101.258 γ = 120
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 mirror 2007-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID
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 1.2 19.75 97.2 0.117 50.6 8.5 27135 27135 10.2
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 1.2 1.22 82.6 0.318 4.2 4.8 883
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.2 19.75 25693 25693 1352 97.16 0.15531 0.15531 0.15448 0.1557 0.17082 0.1716 RANDOM 15.047
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.376 r_dihedral_angle_4_deg 10.895 r_dihedral_angle_3_deg 10.541 r_dihedral_angle_1_deg 6.134 r_sphericity_free 4.689 r_sphericity_bonded 3.888 r_scangle_it 3.479 r_scbond_it 2.953 r_rigid_bond_restr 2.494 r_mcangle_it 1.954
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.376 r_dihedral_angle_4_deg 10.895 r_dihedral_angle_3_deg 10.541 r_dihedral_angle_1_deg 6.134 r_sphericity_free 4.689 r_sphericity_bonded 3.888 r_scangle_it 3.479 r_scbond_it 2.953 r_rigid_bond_restr 2.494 r_mcangle_it 1.954 r_mcbond_it 1.311 r_angle_refined_deg 1.279 r_nbtor_refined 0.311 r_metal_ion_refined 0.265 r_symmetry_hbond_refined 0.247 r_xyhbond_nbd_refined 0.227 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.194 r_chiral_restr 0.094 r_symmetry_metal_ion_refined 0.034 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 671 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing DM phasing HKL-3000 phasing