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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 6 300 7% PEG6000
0.1M HEPES
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.868 α = 90 b = 79.868 β = 90 c = 349.449 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 2018-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97795 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 1.9 72.64 100 0.141 0.964 14.4 25.3 90670
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 1.9 1.93 98.29 2.525 0.668 1.3
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 1.9 72.64 90497 4483 99.89 0.254 0.2518 0.253 0.2903 0.2909 43.051
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] 1.763 1.763 -3.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.228 r_dihedral_angle_4_deg 15.757 r_dihedral_angle_3_deg 13.527 r_dihedral_angle_1_deg 7.958 r_lrange_other 4.826 r_lrange_it 4.743 r_scangle_it 1.571 r_scangle_other 1.571 r_angle_refined_deg 1.411 r_mcangle_it 1.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.228 r_dihedral_angle_4_deg 15.757 r_dihedral_angle_3_deg 13.527 r_dihedral_angle_1_deg 7.958 r_lrange_other 4.826 r_lrange_it 4.743 r_scangle_it 1.571 r_scangle_other 1.571 r_angle_refined_deg 1.411 r_mcangle_it 1.405 r_mcangle_other 1.405 r_angle_other_deg 1.177 r_scbond_it 0.988 r_scbond_other 0.988 r_mcbond_it 0.92 r_mcbond_other 0.92 r_nbd_refined 0.18 r_symmetry_nbd_other 0.179 r_nbd_other 0.158 r_nbtor_refined 0.146 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.14 r_symmetry_nbd_refined 0.106 r_ncsr_local_group_1 0.084 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8044 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing