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Structural Genomics, the Crystal structure of full-length SpoVG from Staphylococcus epidermidis ATCC 12228
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I9X PDB ENTRY 2I9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 0.2M Ammonium sulfate, 0.1M Sodium acetate, 12%(w/v) PEG4000 , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.604 α = 90 b = 63.604 β = 90 c = 98.498 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 ADSC QUANTUM 315 mirror 2006-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97932 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 2.3 44.99 99.7 0.129 18.98 7.2 9486 9486
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 2.3 2.38 97.7 0.531 2.54 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2I9X 2.3 44.99 8946 8946 493 99.7 0.22533 0.22324 0.2239 0.26408 0.2292 RANDOM 30.262
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.123 r_dihedral_angle_4_deg 20.097 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_1_deg 7.584 r_scangle_it 3.514 r_scbond_it 2.205 r_mcangle_it 1.685 r_angle_refined_deg 1.421 r_mcbond_it 0.959 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.123 r_dihedral_angle_4_deg 20.097 r_dihedral_angle_3_deg 18.589 r_dihedral_angle_1_deg 7.584 r_scangle_it 3.514 r_scbond_it 2.205 r_mcangle_it 1.685 r_angle_refined_deg 1.421 r_mcbond_it 0.959 r_nbtor_refined 0.296 r_symmetry_hbond_refined 0.274 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.1 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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 1360 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing