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Structure of native rTp34 from Treponema pallidum from zinc-soaked crystals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 2.4 M Ammonium sulfate, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.451 α = 90 b = 65.921 β = 90 c = 151.744 γ = 90
Symmetry Space Group P 21 21 21
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 CUSTOM-MADE 2006-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.28230 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.87 33.6 99.7 0.106 19.5 7.1 29534 29534 -3 19.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 98.2 0.745 1.8 5.5 1449
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT native protein 1.9 33.6 28101 1413 99.64 0.192 0.19 0.1893 0.233 0.2332 RANDOM 23.776
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] 1.02 -0.45 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.758 r_dihedral_angle_4_deg 19.528 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 6.802 r_scangle_it 3.772 r_scbond_it 2.446 r_angle_refined_deg 1.962 r_mcangle_it 1.564 r_mcbond_it 1.036 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.758 r_dihedral_angle_4_deg 19.528 r_dihedral_angle_3_deg 16.164 r_dihedral_angle_1_deg 6.802 r_scangle_it 3.772 r_scbond_it 2.446 r_angle_refined_deg 1.962 r_mcangle_it 1.564 r_mcbond_it 1.036 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.199 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.145 r_metal_ion_refined 0.075 r_bond_refined_d 0.015 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2485 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling CNS phasing