☰ Navigation Tabs
Crystal structure of a short-chain type dehydrogenase/reductase from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GVC PDB ENTRY 3GVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Internal tracking number 218453, JCSG screen D06: 0.1 M Tris, pH 8.5, 200 mM magnesium chloride, 20% w/v PEG8000, MYMAA.00472.C.A1 PS00808 26.49 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290.0K
Crystal Properties Matthews coefficient Solvent content 2.31 46.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.67 α = 90 b = 122.07 β = 101.03 c = 125.29 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 ADSC QUANTUM 315r 2011-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
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 2.5 19.92 97.9 0.119 8.96 2.632 71016 69690 -3 -3 24.7
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 2.5 2.56 92.9 0.389 2.4 2.238 10922
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 MR THROUGHOUT PDB ENTRY 3GVC 2.5 19.92 2 71016 69690 3526 97.9 0.183 0.183 0.18 0.1792 0.244 0.2378 RANDOM 16.74
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] 0.58 -0.03 -0.47 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.477 r_dihedral_angle_4_deg 16.05 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_1_deg 5.99 r_angle_refined_deg 1.363 r_angle_other_deg 0.942 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.477 r_dihedral_angle_4_deg 16.05 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_1_deg 5.99 r_angle_refined_deg 1.363 r_angle_other_deg 0.942 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15121 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 100
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling