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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 2.42 49.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.74 α = 90 b = 79.74 β = 90 c = 349.5 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 PILATUS 6M 2015-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.97 77.863 99.4 1 21.8 3.81 80616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.01 0.472 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 1.97 77.863 80615 3899 99.314 0.232 0.2304 0.2309 0.2662 0.2666 43.851
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] 2.005 2.005 -4.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.344 r_dihedral_angle_4_deg 13.978 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 8.111 r_lrange_it 4.071 r_lrange_other 4.043 r_scangle_it 1.879 r_scangle_other 1.879 r_mcangle_it 1.746 r_mcangle_other 1.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.344 r_dihedral_angle_4_deg 13.978 r_dihedral_angle_3_deg 12.743 r_dihedral_angle_1_deg 8.111 r_lrange_it 4.071 r_lrange_other 4.043 r_scangle_it 1.879 r_scangle_other 1.879 r_mcangle_it 1.746 r_mcangle_other 1.746 r_angle_refined_deg 1.35 r_scbond_it 1.219 r_scbond_other 1.215 r_mcbond_it 1.19 r_mcbond_other 1.19 r_angle_other_deg 1.17 r_symmetry_xyhbond_nbd_refined 0.232 r_nbd_refined 0.181 r_symmetry_nbd_other 0.174 r_nbd_other 0.162 r_xyhbond_nbd_refined 0.151 r_nbtor_refined 0.147 r_ncsr_local_group_1 0.077 r_symmetry_nbd_refined 0.074 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.054 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 8046 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing