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Mycobacterium abscessus NadD in complex with nicotinic acid adenine dinucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.1M Tris-HCl pH 8.5, 20% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.09 α = 90 b = 58.438 β = 90.74 c = 109.884 γ = 90
Symmetry Space Group P 1 21 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 RAYONIX MX300-HS 2015-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.22 71.08 97.3 0.108 0.127 12.24 3.8 43720 -3 44.242
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.28 98.1 1.03 1.198 2.23 3.8
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 4YMI 2.22 71.08 41530 2223 97.31 0.2365 0.234 0.237 0.2815 0.2821 RANDOM 45.08
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] 1.77 0.16 -0.75 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.767 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 6.007 r_mcangle_it 3.495 r_mcbond_it 2.094 r_mcbond_other 2.094 r_angle_refined_deg 1.197 r_angle_other_deg 0.906 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.767 r_dihedral_angle_4_deg 15.607 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 6.007 r_mcangle_it 3.495 r_mcbond_it 2.094 r_mcbond_other 2.094 r_angle_refined_deg 1.197 r_angle_other_deg 0.906 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5646 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 176
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction