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Structural Genomics, the crystal structure of SpoVG conserved domain from Staphylococcus epidermidis ATCC 12228
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 5%(w/v) isopropanol, 0.1M HEPES pH 7.5, 10%(v/w) PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.55 α = 90 b = 64.55 β = 90 c = 97.711 γ = 90
Symmetry Space Group P 41 21 2
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 SBC-3 mirror 2006-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97918 APS 19-BM
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 1.8 26.51 99.7 0.063 31.62 6.1 19791 19791
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 1.8 1.84 100 0.459 3.73 6.2
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 (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 1.8 24.85 18720 18719 1010 99.69 0.18981 0.18806 0.1869 0.2226 0.2195 RANDOM 25.952
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.612 r_dihedral_angle_4_deg 17.717 r_dihedral_angle_3_deg 15.525 r_dihedral_angle_1_deg 7.527 r_scangle_it 4.89 r_scbond_it 3.087 r_mcangle_it 2.16 r_angle_refined_deg 1.491 r_mcbond_it 1.368 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.612 r_dihedral_angle_4_deg 17.717 r_dihedral_angle_3_deg 15.525 r_dihedral_angle_1_deg 7.527 r_scangle_it 4.89 r_scbond_it 3.087 r_mcangle_it 2.16 r_angle_refined_deg 1.491 r_mcbond_it 1.368 r_nbtor_refined 0.303 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.123 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_refined 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1354 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building