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Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DFU 2dfu molecule A, protein only
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 MymaA.00471.a.A1 PW30262 at 26.1 mg/mL against PACT screen condition A12, 10 mM ZnCl2, 0.1 M NaOAc pH 5.0, 20% PEG 6000 and cryo-protected with 25% ethylene glycol, crystal tracking ID 218461a12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.7 α = 90 b = 104.93 β = 90 c = 136.97 γ = 90
Symmetry Space Group I 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 CCD RIGAKU SATURN 944+ 2011-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.05 50 98.5 0.076 14.42 4.2 22070 21732 -3 31.963
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 2.05 2.1 91.9 0.461 2.9 2.8 1597
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2dfu molecule A, protein only 2.05 50 21644 1119 98.07 0.185 0.1826 0.2294 0.1997 RANDOM 26.6039
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] -0.02 1.14 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.929 r_dihedral_angle_4_deg 18.091 r_dihedral_angle_3_deg 13.046 r_dihedral_angle_1_deg 6.641 r_scangle_it 2.717 r_scbond_it 1.668 r_angle_refined_deg 1.377 r_mcangle_it 1.073 r_mcbond_it 0.62 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.929 r_dihedral_angle_4_deg 18.091 r_dihedral_angle_3_deg 13.046 r_dihedral_angle_1_deg 6.641 r_scangle_it 2.717 r_scbond_it 1.668 r_angle_refined_deg 1.377 r_mcangle_it 1.073 r_mcbond_it 0.62 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1862 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 14
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction