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Apo NIS synthetase DesD variant R306Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NL2 PDB entry 6NL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.08 mM Tris-HCl, pH 8.5, 160 mM magnesium chloride, 24% PEG4000, 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.417 α = 90 b = 98.921 β = 90 c = 183.352 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CMOS RDI CMOS_8M 2016-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.45 61.12 99.9 0.153 0.172 0.063 0.993 7.7 7.4 50570
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 2.45 2.53 0.534 0.964 3.4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 6NL2 2.45 59.47 50526 2494 99.8 0.2 0.206 0.27 0.2729 46.18
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] -8.804 34.526 -25.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 20.009 r_dihedral_angle_3_deg 16.83 r_dihedral_angle_1_deg 8.055 r_scangle_it 2.781 r_scangle_other 2.78 r_mcangle_it 2.607 r_mcangle_other 2.605 r_angle_other_deg 2.4 r_angle_refined_deg 1.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 20.009 r_dihedral_angle_3_deg 16.83 r_dihedral_angle_1_deg 8.055 r_scangle_it 2.781 r_scangle_other 2.78 r_mcangle_it 2.607 r_mcangle_other 2.605 r_angle_other_deg 2.4 r_angle_refined_deg 1.817 r_scbond_it 1.68 r_scbond_other 1.679 r_mcbond_it 1.504 r_mcbond_other 1.502 r_nbd_other 0.226 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.171 r_chiral_restr 0.08 r_bond_other_d 0.035 r_bond_refined_d 0.013 r_gen_planes_other 0.012 r_gen_planes_refined 0.009 r_xyhbond_nbd_other 0.006 r_nbtor_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_long_range_B_refined 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 9354 Nucleic Acid Atoms Solvent Atoms 640 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing