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Mycobacterium abscessus NadD in complex with Mg-ATP, space group I41
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, SITTING DROP 7.6 298 0.02M HEPES pH 7.6, 14% PEG3350, 0.002M Mg-ATP
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.098 α = 90 b = 67.098 β = 90 c = 229.538 γ = 90
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 2015-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 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 2.28 57.38 99.1 0.067 0.075 16.8 5.2 22829 -3 54.114
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 2.28 2.34 98.7 1.04 1.155 1.69 5.2
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 2.28 57.38 21694 1139 99.1 0.1961 0.1934 0.1989 0.2483 0.2559 RANDOM 55.888
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] 1.24 1.24 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.411 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_1_deg 6.222 r_mcangle_it 4.585 r_mcbond_it 2.89 r_mcbond_other 2.889 r_angle_refined_deg 1.279 r_angle_other_deg 0.902 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.411 r_dihedral_angle_4_deg 19.942 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_1_deg 6.222 r_mcangle_it 4.585 r_mcbond_it 2.89 r_mcbond_other 2.889 r_angle_refined_deg 1.279 r_angle_other_deg 0.902 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2735 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 64
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction