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Crystal structure of a putative short chain dehydrogenase or reductase from Mycobacterium abscessus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PK0 PDB ENTRY 3PK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MyabA.01365.a.A1 PS00935 at 68.8 mg/mL against JCSG+ B12: 0.2 M potassium citrate, 20% PEG 3350 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 219942b12, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.28 71.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.55 α = 90 b = 208.55 β = 90 c = 94.67 γ = 90
Symmetry Space Group P 43 21 2
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 315r 2011-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 2.15 50 99.9 0.119 16.32 10.6 113114 113051 -3 28.642
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 2.15 2.21 99.9 0.543 4.04 8.2 8232
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 PDB ENTRY 3PK0 2.15 50 112763 5653 99.63 0.1555 0.1543 0.1543 0.1781 0.1786 RANDOM 22.2602
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] -0.36 -0.36 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_4_deg 18.647 r_dihedral_angle_3_deg 12.952 r_dihedral_angle_1_deg 5.415 r_scangle_it 4.095 r_scbond_it 2.358 r_angle_refined_deg 1.305 r_mcangle_it 1.296 r_mcbond_it 0.685 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.647 r_dihedral_angle_4_deg 18.647 r_dihedral_angle_3_deg 12.952 r_dihedral_angle_1_deg 5.415 r_scangle_it 4.095 r_scbond_it 2.358 r_angle_refined_deg 1.305 r_mcangle_it 1.296 r_mcbond_it 0.685 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7314 Nucleic Acid Atoms Solvent Atoms 823 Heterogen Atoms 128
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction