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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 49.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.055 α = 90 b = 80.055 β = 90 c = 349.751 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 2.11 66.082 100 0.125 0.895 11.4 12.8 67026
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 2.11 2.15 2.359 0.61 1
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 2.11 66.082 66825 3412 99.863 0.242 0.2401 0.2383 0.2661 0.262 54.128
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] 1.774 1.774 -3.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.336 r_dihedral_angle_4_deg 14.66 r_dihedral_angle_3_deg 13.616 r_dihedral_angle_1_deg 8.155 r_lrange_it 2.526 r_lrange_other 2.524 r_angle_refined_deg 1.434 r_mcangle_other 1.229 r_mcangle_it 1.228 r_scangle_it 1.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.336 r_dihedral_angle_4_deg 14.66 r_dihedral_angle_3_deg 13.616 r_dihedral_angle_1_deg 8.155 r_lrange_it 2.526 r_lrange_other 2.524 r_angle_refined_deg 1.434 r_mcangle_other 1.229 r_mcangle_it 1.228 r_scangle_it 1.196 r_scangle_other 1.196 r_angle_other_deg 1.194 r_mcbond_it 0.762 r_mcbond_other 0.761 r_scbond_it 0.738 r_scbond_other 0.738 r_nbd_refined 0.188 r_nbd_other 0.185 r_symmetry_nbd_refined 0.18 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.15 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.121 r_ncsr_local_group_1 0.077 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.06 r_bond_refined_d 0.006 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 8040 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing