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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 1GGQ Partially refined model for VspA 34-214, derived by molecular replacement starting from Borrelia burgdorferi OspC, strain B31 (PDB ID 1GGQ)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 294 25% (w/v) PEG 4000, 0.1 M LiCl, and 0.1 mM taurine, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.857 α = 90 b = 34.213 β = 112.68 c = 99.386 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 CCD ADSC QUANTUM 315 Si Monochromator 2004-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 50 95.7 0.05 0.047 26 2.93 26408 26408
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.3 84.5 0.166 0.161 3.4 2.68 2308
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 Partially refined model for VspA 34-214, derived by molecular replacement starting from Borrelia burgdorferi OspC, strain B31 (PDB ID 1GGQ) 2.22 50 26240 25078 1329 95.57 0.20875 0.20875 0.20577 0.2112 0.26486 0.265 RANDOM 20.726
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] -1.21 -1.82 2.03 -2.22
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.05 r_mcangle_it 2.779 r_scbond_it 2.065 r_mcbond_it 1.92 r_angle_refined_deg 1.258 r_dihedral_angle_1_deg 0.764 r_angle_other_deg 0.752 r_nbd_other 0.207 r_symmetry_hbond_refined 0.199 r_symmetry_vdw_other 0.195
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.05 r_mcangle_it 2.779 r_scbond_it 2.065 r_mcbond_it 1.92 r_angle_refined_deg 1.258 r_dihedral_angle_1_deg 0.764 r_angle_other_deg 0.752 r_nbd_other 0.207 r_symmetry_hbond_refined 0.199 r_symmetry_vdw_other 0.195 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.162 r_xyhbond_nbd_refined 0.157 r_nbtor_other 0.086 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4508 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing