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Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YJG PDB ENTRY 1YJG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 28% (w/v) polyethylene glycol (PEG), 80 mM Tris HCl, 15% (v/v) glycerol, 100 mM NiCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 241.835 α = 90 b = 69.105 β = 104.95 c = 87.578 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2000-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12C 1.0 NSLS X12C
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 2.7 50 98.9 0.042 12.5 38032 38032
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 2.7 2.8 92 92 0.147
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1YJG 2.7 50 38031 38031 1902 98.7 0.219 0.219 0.216 0.2135 0.272 0.2595 RANDOM 19.313
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] -1.04 -0.92 1.91 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.121 r_scangle_it 2.486 r_scbond_it 2.429 r_angle_refined_deg 1.544 r_mcangle_it 0.589 r_symmetry_hbond_refined 0.383 r_mcbond_it 0.263 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.121 r_scangle_it 2.486 r_scbond_it 2.429 r_angle_refined_deg 1.544 r_mcangle_it 0.589 r_symmetry_hbond_refined 0.383 r_mcbond_it 0.263 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9456 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction