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The structure of NanH in complex with Neu5,9Ac
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M HEPES: NaOH pH 7.5, and 20% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.037 α = 90 b = 64.261 β = 102.7 c = 66.273 γ = 90
Symmetry Space Group C 1 2 1
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 200K 2021-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.514
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 1.89 22.9 100 0.981 11.6 4.6 30625
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 1.894 1.943 0.881
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.89 22.9 28261 1462 96.65 0.18733 0.18592 0.1859 0.21465 0.2146 RANDOM 21.56
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] -0.08 0.19 -0.33 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.409 r_dihedral_angle_3_deg 11.915 r_dihedral_angle_4_deg 8.36 r_dihedral_angle_1_deg 7.865 r_long_range_B_refined 3.796 r_mcangle_it 1.623 r_scbond_it 1.431 r_angle_refined_deg 1.182 r_mcbond_it 1.107 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.409 r_dihedral_angle_3_deg 11.915 r_dihedral_angle_4_deg 8.36 r_dihedral_angle_1_deg 7.865 r_long_range_B_refined 3.796 r_mcangle_it 1.623 r_scbond_it 1.431 r_angle_refined_deg 1.182 r_mcbond_it 1.107 r_chiral_restr 0.086 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2831 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing