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Mutant Slackia exigua KARI DDV in complex with NAD and an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KQW PDB Entry 4KQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 297 Unbuffered 0.1 M potassium thiocyanate solution with 30% w/v polyethylene glycol
monomethyl ether 2000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.07 40.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.985 α = 90 b = 105.346 β = 90 c = 122.357 γ = 90
Symmetry Space Group P 21 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 100 PIXEL DECTRIS PILATUS 6M 2012-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 79.833 98.9 0.118 0.118 6.2 3.3 59961 59961 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.5 0.711 0.711 3.4 8689
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB Entry 4KQW 1.8 79.83 -3 78635 56866 3035 98.6 0.20396 0.20396 0.20141 0.2013 0.25202 0.2518 RANDOM 20.062
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] 3.49 -1.68 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_4_deg 17.412 r_dihedral_angle_3_deg 15.024 r_dihedral_angle_1_deg 6.28 r_angle_refined_deg 2.108 r_chiral_restr 0.15 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.26 r_dihedral_angle_4_deg 17.412 r_dihedral_angle_3_deg 15.024 r_dihedral_angle_1_deg 6.28 r_angle_refined_deg 2.108 r_chiral_restr 0.15 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5089 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 128
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XSCALE data scaling SCALA data scaling