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Crystal structure of fumarase Fum from Mycobacterium marinum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NO9 pdb entry 3no9, molecule A residues 43 to 393
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 MymaA.01507.a.A1 PS00842 at 51.1 mg/mL against PACT screen condition A7, 0.2 M NaCl, 0.1 M NaOAc pH 5.0, 20% PEG 6000 soaked into PACT A7 with 25% EG as cryo-protectant, crystal tracking ID 218662a7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.88 α = 90 b = 114.08 β = 107.01 c = 98.84 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 2010-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97946 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 1.85 50 99.9 0.09 14.51 4.6 176835 176663 -3 22.3
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 1.85 1.9 100 0.505 3.1 4.6
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 3no9, molecule A residues 43 to 393 1.85 50 176519 8834 99.9 0.157 0.155 0.1601 0.188 0.1928 17.28
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] -0.34 0.79 -0.75 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.664 r_dihedral_angle_4_deg 17.533 r_dihedral_angle_3_deg 12.559 r_dihedral_angle_1_deg 5.079 r_scangle_it 3.357 r_scbond_it 2 r_angle_refined_deg 1.314 r_mcangle_it 1.203 r_mcbond_it 0.689 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.664 r_dihedral_angle_4_deg 17.533 r_dihedral_angle_3_deg 12.559 r_dihedral_angle_1_deg 5.079 r_scangle_it 3.357 r_scbond_it 2 r_angle_refined_deg 1.314 r_mcangle_it 1.203 r_mcbond_it 0.689 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12804 Nucleic Acid Atoms Solvent Atoms 1684 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction