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The crystal structure of KanD2 in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 PEG 8000, imidazole, calcium acetate, NAD
Crystal Properties Matthews coefficient Solvent content 3.39 63.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.469 α = 90 b = 119.469 β = 90 c = 131.435 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 270 2017-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 50 100 0.085 23.3 11.1 27212
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 100 0.918 2.5 11.3
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 (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 4H3V 2.8 48.18 25759 1353 99.71 0.1985 0.1962 0.2023 0.2445 0.2455 RANDOM 79.263
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] -0.34 -0.34 -0.34 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.476 r_dihedral_angle_4_deg 22.531 r_dihedral_angle_3_deg 17.431 r_dihedral_angle_1_deg 6.584 r_angle_refined_deg 1.68 r_angle_other_deg 1.04 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.476 r_dihedral_angle_4_deg 22.531 r_dihedral_angle_3_deg 17.431 r_dihedral_angle_1_deg 6.584 r_angle_refined_deg 1.68 r_angle_other_deg 1.04 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5168 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing