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The structure of T. forsythia NanH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 290 7% PEG6000
0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.895 α = 90 b = 79.895 β = 90 c = 349.328 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 6M 2017-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.659 79.89 100 0.168 0.992 6.9 12.1 135097
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 99.21 0.851 0.435 0.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4bbw 1.659 78.005 133326 6556 98.77 0.224 0.2218 0.2155 0.2727 0.2595 29.929
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] 0.764 0.764 -1.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 12.289 r_lrange_other 11.131 r_lrange_it 11.082 r_scangle_it 10.725 r_scangle_other 10.725 r_scbond_it 10.58 r_scbond_other 10.579 r_dihedral_angle_1_deg 8.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.129 r_dihedral_angle_4_deg 14.714 r_dihedral_angle_3_deg 12.289 r_lrange_other 11.131 r_lrange_it 11.082 r_scangle_it 10.725 r_scangle_other 10.725 r_scbond_it 10.58 r_scbond_other 10.579 r_dihedral_angle_1_deg 8.163 r_mcbond_it 7.106 r_mcbond_other 7.106 r_mcangle_it 6.747 r_mcangle_other 6.747 r_angle_refined_deg 1.681 r_angle_other_deg 1.357 r_nbd_refined 0.198 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.178 r_nbd_other 0.176 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.126 r_symmetry_xyhbond_nbd_other 0.105 r_ncsr_local_group_1 0.089 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8046 Nucleic Acid Atoms Solvent Atoms 704 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing