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Crystal structure of fumarate hydratase Fum from Mycobacterium abscessus with malate bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RD8 PDB ENTRY 3RD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 MyabA.01507.a.A1 PW30392 at 29.54 mg/mL against Wizard III/IV screen condition G8, 2.1 M DL Malic acid, pH 7.0 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220029g8, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.8 α = 90 b = 156.92 β = 90 c = 57.76 γ = 90
Symmetry Space Group P 21 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 2011-03-26 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 2.3 50 97.4 0.147 11.37 5.5 40352 39296 -3 24.91
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) 2.3 2.36 93.1 0.527 3.19 4.8 2719
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 3RD8 2.3 50 39144 1950 97.01 0.1624 0.1601 0.1627 0.207 0.2077 RANDOM 17.2985
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] -1.11 -0.94 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.474 r_dihedral_angle_4_deg 18.183 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 5.557 r_scangle_it 2.744 r_scbond_it 1.707 r_angle_refined_deg 1.38 r_mcangle_it 0.835 r_mcbond_it 0.471 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.474 r_dihedral_angle_4_deg 18.183 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 5.557 r_scangle_it 2.744 r_scbond_it 1.707 r_angle_refined_deg 1.38 r_mcangle_it 0.835 r_mcbond_it 0.471 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6761 Nucleic Acid Atoms Solvent Atoms 538 Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction