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Crystal structure of Maleylacetoacetate isomerase from Anaeromyxobacter dehalogenans 2CP-1, TARGET EFI-507175, with bound dicarboxyethyl glutathione and citrate in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IGJ PDB ENTRY 4IGJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.2 M ammonium citrate dibasic, pH 5.0, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.03 39.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.508 α = 90 b = 80.498 β = 90 c = 87.689 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX225HE 2013-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.5 50 99.9 0.104 17.4 7.3 72421 72323
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 1.5 1.53 100 0.687 3.1 7.3
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 4IGJ 1.5 31.72 68606 3643 99.68 0.16068 0.15963 0.1593 0.17999 0.18 RANDOM 17.553
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] 0.55 -0.58 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.666 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 12.648 r_dihedral_angle_1_deg 6.191 r_angle_refined_deg 1.499 r_angle_other_deg 0.759 r_chiral_restr 0.103 r_gen_planes_refined 0.015 r_bond_refined_d 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.666 r_dihedral_angle_4_deg 18.848 r_dihedral_angle_3_deg 12.648 r_dihedral_angle_1_deg 6.191 r_angle_refined_deg 1.499 r_angle_other_deg 0.759 r_chiral_restr 0.103 r_gen_planes_refined 0.015 r_bond_refined_d 0.012 r_gen_planes_other 0.002 r_bond_other_d 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3467 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 75
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling