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Crystal structure of antigen TpF1 from Treponema pallidum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JI4 PDB entry 1JI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 10% PEG 6000, 8% ethylene glycol, 0.1 M Tris buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.77 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.921 α = 90 b = 184.921 β = 90 c = 154.883 γ = 120
Symmetry Space Group P 3 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 MARRESEARCH 2004-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2 ELETTRA 5.2R
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 2.45 185 95.7 0.072 8.5 5.1 111030 111030 56.6
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) 2.45 2.55 70.8 0.37 1.5 3.9 11886
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 1JI4 2.5 59.37 105521 105521 10614 99.9 0.227 0.227 0.227 0.252 0.252 RANDOM 40.4
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] 0.4 4.95 0.4 -0.81
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18 c_scangle_it 2.86 c_scbond_it 1.91 c_mcangle_it 1.76 c_angle_deg 1.2 c_mcbond_it 1.08 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 18 c_scangle_it 2.86 c_scbond_it 1.91 c_mcangle_it 1.76 c_angle_deg 1.2 c_mcbond_it 1.08 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18986 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 16
Software Software Software Name Purpose CNS refinement MAR345 data collection CCP4 data scaling AMoRE phasing