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Crystal structure of Tannerella forsythia Apo HmuY analog (TFO)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 Sodium malonate, Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.05 α = 90 b = 68.05 β = 90 c = 90.22 γ = 120
Symmetry Space Group P 31 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 PILATUS 6M 2016-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92818 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.47 49.34 100 0.033 0.011 1 30.2 9.8 41705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 99.9 2.1 0.76 0.6 1.1 9
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 3UU2 1.47 49.34 39662 2004 99.97 0.18631 0.18453 0.1927 0.21908 0.2251 RANDOM 32.101
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] 0.55 0.28 0.55 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.241 r_dihedral_angle_4_deg 15.035 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 6.554 r_long_range_B_refined 6.253 r_long_range_B_other 5.854 r_scangle_other 4.313 r_scbond_it 2.798 r_scbond_other 2.792 r_mcangle_it 2.575
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.241 r_dihedral_angle_4_deg 15.035 r_dihedral_angle_3_deg 12.935 r_dihedral_angle_1_deg 6.554 r_long_range_B_refined 6.253 r_long_range_B_other 5.854 r_scangle_other 4.313 r_scbond_it 2.798 r_scbond_other 2.792 r_mcangle_it 2.575 r_mcangle_other 2.575 r_mcbond_it 1.816 r_mcbond_other 1.814 r_angle_refined_deg 1.502 r_angle_other_deg 0.893 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 1539 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing