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Crystal structure of 4-methylmuconolactone methylisomerase in complex with 3-methylmuconolactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HDS PDB ENTRY 3HDS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 5 292 25% PEG 1500, 0.1M MMT, hanging drop, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.36 47.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.76 α = 90 b = 84 β = 90 c = 150.05 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 315r 2008-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.10505 ESRF ID23-1
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 1.4 42 99.8 0.089 15.87 9.9 101311 -3
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 1.4 1.5 99.5 0.682 0.68 3.5 9.9
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 3HDS 1.4 40.88 96243 5065 99.84 0.17895 0.17744 0.1751 0.2076 0.2066 RANDOM 17.555
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] 0.11 0.36 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.364 r_dihedral_angle_4_deg 17.969 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_1_deg 5.866 r_scangle_it 4.407 r_scbond_it 2.791 r_mcangle_it 2.052 r_angle_refined_deg 1.895 r_mcbond_it 1.209 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.364 r_dihedral_angle_4_deg 17.969 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_1_deg 5.866 r_scangle_it 4.407 r_scbond_it 2.791 r_mcangle_it 2.052 r_angle_refined_deg 1.895 r_mcbond_it 1.209 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 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 3718 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 44
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection