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Crystal structure of the TPM domain from the Rhodothermus marinus protein Rhom172_1776
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ANP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 293 12% PEG 6000, 5% isopropanol, 0.1 M Bis-tris-propane pH 8.4
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.78 α = 90 b = 37.56 β = 118.15 c = 48.53 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 PIXEL DECTRIS EIGER X 9M convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors 2021-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.885601 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.1 42.79 99 0.039 0.999 18.5 6.6 54711 18.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 95.4 1.021 0.679 1.5 5.6
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 MOLECULAR REPLACEMENT THROUGHOUT 5ANP 1.1 42.79 51975 2736 99.2 0.19216 0.1907 0.1934 0.2206 0.2216 RANDOM 17.477
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] 0.53 -0.34 0.3 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.523 r_dihedral_angle_4_deg 14.8 r_dihedral_angle_3_deg 12 r_dihedral_angle_1_deg 6.001 r_long_range_B_refined 5.282 r_long_range_B_other 5.209 r_scangle_other 3.829 r_scbond_it 2.634 r_scbond_other 2.631 r_mcangle_it 2.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.523 r_dihedral_angle_4_deg 14.8 r_dihedral_angle_3_deg 12 r_dihedral_angle_1_deg 6.001 r_long_range_B_refined 5.282 r_long_range_B_other 5.209 r_scangle_other 3.829 r_scbond_it 2.634 r_scbond_other 2.631 r_mcangle_it 2.166 r_mcangle_other 2.166 r_angle_refined_deg 1.846 r_angle_other_deg 1.564 r_mcbond_it 1.524 r_mcbond_other 1.52 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1082 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data scaling XDS data reduction MoRDa phasing ARP/wARP model building Coot model building