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Crystal structure of 4-methylmuconolactone methylisomerase (H52A) in complex with 4-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 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.17 α = 90 b = 84.36 β = 90 c = 150.47 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 2009-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97900 ESRF ID14-4
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 1.9 75.24 99.4 0.113 14.71 7.23 41197 -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 1.9 2 99 0.564 3.5 7.15
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 1.9 40.62 39116 2079 99.27 0.18698 0.18463 0.1821 0.23131 0.2307 RANDOM 19.01
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] 0.2 0.65 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.453 r_dihedral_angle_4_deg 18.881 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_1_deg 5.722 r_scangle_it 4.049 r_scbond_it 2.58 r_mcangle_it 1.683 r_angle_refined_deg 1.579 r_mcbond_it 0.969 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.453 r_dihedral_angle_4_deg 18.881 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_1_deg 5.722 r_scangle_it 4.049 r_scbond_it 2.58 r_mcangle_it 1.683 r_angle_refined_deg 1.579 r_mcbond_it 0.969 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 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 3685 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 77
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction