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Crystal structure of fumarate hydratase class II Mycobacterium smegmatis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NO9 PDB ENTRY 3NO9, modified by CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 MOLECULAR DIMENSIONS PACT SCREEN F9: 200MM NA/K TARTRATE, 100M BISTRISPROPANE PH 6.5, 20% PEG 3350; MYSMA.01507.A.A1 PS00681 AT 67.55MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.66 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.49 α = 90 b = 105.25 β = 90 c = 139.02 γ = 90
Symmetry Space Group I 2 2 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 RIGAKU SATURN 944+ 2010-08-04 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) R Sym 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 2.2 50 97.5 0.089 0.089 14.11 4.6 27400 26708 -3 34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 99.2 0.523 0.523 2.8 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3NO9, modified by CHAINSAW 2.2 50 27400 26630 1332 97.2 0.174 0.173 0.1721 0.203 0.2025 RANDOM 25.36
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] -0.35 1.64 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.415 r_dihedral_angle_4_deg 15.944 r_dihedral_angle_3_deg 12.411 r_dihedral_angle_1_deg 5.304 r_scangle_it 2.713 r_scbond_it 1.743 r_angle_refined_deg 1.335 r_angle_other_deg 0.965 r_mcangle_it 0.892 r_mcbond_it 0.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.415 r_dihedral_angle_4_deg 15.944 r_dihedral_angle_3_deg 12.411 r_dihedral_angle_1_deg 5.304 r_scangle_it 2.713 r_scbond_it 1.743 r_angle_refined_deg 1.335 r_angle_other_deg 0.965 r_mcangle_it 0.892 r_mcbond_it 0.507 r_mcbond_other 0.134 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3312 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling