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Crystal structure of Maleylacetoacetate isomerase from Methylobacteriu extorquens AM1 WITH BOUND MALONATE AND GSH (TARGET EFI-507068)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PX1 PDB ENTRY 4PX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PROTEIN (10 MM TRIS, 150 MM NACL, 5% GLYCEROL, 5 MM DTT); RESERVOIR (0.1 M HEPES-NAOH, PH 7.0, 1.1M SODIUM MALONATE, 0.5% (v/v) Jeffamine ED-2001 (MCSG2 B10), 10 MM GSH; CRYOPROTECTION: (RESERVOIR), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 3.08 60.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.628 α = 90 b = 109.628 β = 90 c = 185.367 γ = 120
Symmetry Space Group P 65 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 ADSC QUANTUM 315 MIRRORS 2014-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 50 99.7 0.101 23.4 14.4 61218 -5 21.628
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 1.8 1.83 100 2 14.3
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 4PX1 1.8 50 59371 1824 99.69 0.14506 0.14418 0.1585 0.17421 0.1884 RANDOM 31.344
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] 0.68 0.34 0.68 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.855 r_dihedral_angle_4_deg 18.984 r_dihedral_angle_3_deg 12.062 r_long_range_B_other 9.118 r_long_range_B_refined 9.116 r_scangle_other 6.835 r_scbond_it 6.09 r_scbond_other 6.086 r_dihedral_angle_1_deg 4.962 r_mcangle_other 4.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.855 r_dihedral_angle_4_deg 18.984 r_dihedral_angle_3_deg 12.062 r_long_range_B_other 9.118 r_long_range_B_refined 9.116 r_scangle_other 6.835 r_scbond_it 6.09 r_scbond_other 6.086 r_dihedral_angle_1_deg 4.962 r_mcangle_other 4.442 r_mcangle_it 4.359 r_mcbond_it 4.031 r_mcbond_other 3.833 r_angle_refined_deg 1.195 r_angle_other_deg 0.783 r_chiral_restr 0.071 r_bond_refined_d 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3324 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 86
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling