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1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 295 Protein: 14.6 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: PACT (A7), 0.2M Sodium chloride, 0.1M Sodium acetate pH (5.0), 20% (w/v) PEG 6000.
Crystal Properties Matthews coefficient Solvent content 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.385 α = 90 b = 111.712 β = 100.42 c = 96.954 γ = 90
Symmetry Space Group P 1 21 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 300 mm CCD C(111) 2017-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 1.36 30 99.1 0.087 0.087 0.047 15.4 4.3 280381 -3 10.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.38 96.5 0.715 0.715 0.426 0.607 2.07 3.7
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 3S9Z 1.36 29.62 266396 13944 98.93 0.14453 0.14333 0.1527 0.16782 0.1744 RANDOM 11.977
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] 0.02 -0.13 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.676 r_dihedral_angle_4_deg 13.994 r_dihedral_angle_3_deg 9.905 r_long_range_B_refined 4.605 r_long_range_B_other 3.997 r_dihedral_angle_1_deg 3.926 r_scangle_other 1.773 r_angle_refined_deg 1.446 r_scbond_it 1.149 r_scbond_other 1.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.676 r_dihedral_angle_4_deg 13.994 r_dihedral_angle_3_deg 9.905 r_long_range_B_refined 4.605 r_long_range_B_other 3.997 r_dihedral_angle_1_deg 3.926 r_scangle_other 1.773 r_angle_refined_deg 1.446 r_scbond_it 1.149 r_scbond_other 1.149 r_mcangle_it 1.094 r_mcangle_other 1.094 r_angle_other_deg 0.867 r_mcbond_it 0.664 r_mcbond_other 0.664 r_chiral_restr 0.093 r_gen_planes_refined 0.024 r_gen_planes_other 0.021 r_bond_refined_d 0.009 r_bond_other_d 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 11050 Nucleic Acid Atoms Solvent Atoms 2247 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing