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Crystal structure of human fumarate hydratase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YFM PDB entry 1YFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 20% PEG 3350, 10% ethanediol, 0.2 M sodium acetate, 0.1 M bis-tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.483 α = 90 b = 188.483 β = 90 c = 114.632 γ = 120
Symmetry Space Group P 32 2 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 MARMOSAIC 225 mm CCD 2008-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
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 1.95 25 99.3 0.14 9.7 6.2 168629 21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 96.8 2 5 23857
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 (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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1YFM 1.95 25 166623 1995 99.28 0.19728 0.19728 0.19673 0.2004 0.24408 0.2451 RANDOM 19.909
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] -0.51 -0.26 -0.51 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.248 r_dihedral_angle_4_deg 20.659 r_dihedral_angle_3_deg 13.361 r_dihedral_angle_1_deg 5.715 r_scangle_it 2.602 r_scbond_it 1.826 r_angle_refined_deg 1.419 r_mcangle_it 1.052 r_angle_other_deg 1.029 r_mcbond_it 0.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.248 r_dihedral_angle_4_deg 20.659 r_dihedral_angle_3_deg 13.361 r_dihedral_angle_1_deg 5.715 r_scangle_it 2.602 r_scbond_it 1.826 r_angle_refined_deg 1.419 r_mcangle_it 1.052 r_angle_other_deg 1.029 r_mcbond_it 0.722 r_symmetry_vdw_other 0.228 r_nbd_refined 0.204 r_mcbond_other 0.197 r_nbd_other 0.184 r_symmetry_hbond_refined 0.175 r_symmetry_vdw_refined 0.171 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.085 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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 13145 Nucleic Acid Atoms Solvent Atoms 655 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing