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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 2.44 49.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.059 α = 90 b = 80.059 β = 90 c = 349.789 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 2.06 72.901 100 0.158 0.999 14.8 25.6 71921
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 2.06 2.1 2.964 0.797 1.4
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 2.06 72.901 71564 3626 99.695 0.246 0.2448 0.2424 0.2786 0.2755 49.091
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] 1.909 1.909 -3.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 16.164 r_dihedral_angle_3_deg 13.597 r_dihedral_angle_1_deg 7.832 r_lrange_it 5.618 r_lrange_other 5.562 r_scangle_it 1.81 r_scangle_other 1.809 r_mcangle_it 1.546 r_mcangle_other 1.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 16.164 r_dihedral_angle_3_deg 13.597 r_dihedral_angle_1_deg 7.832 r_lrange_it 5.618 r_lrange_other 5.562 r_scangle_it 1.81 r_scangle_other 1.809 r_mcangle_it 1.546 r_mcangle_other 1.545 r_angle_refined_deg 1.306 r_angle_other_deg 1.125 r_scbond_it 1.115 r_scbond_other 1.115 r_mcbond_it 0.989 r_mcbond_other 0.989 r_nbd_refined 0.176 r_symmetry_nbd_other 0.174 r_nbd_other 0.162 r_nbtor_refined 0.145 r_xyhbond_nbd_refined 0.134 r_symmetry_xyhbond_nbd_refined 0.118 r_ncsr_local_group_1 0.083 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.047 r_symmetry_xyhbond_nbd_other 0.044 r_symmetry_nbd_refined 0.038 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8019 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing