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Structural insights for non-natural cofactor binding by the L310R/Q401C mutant of malic enzyme from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 297 0.7 M Lithium chloride,0.1 M Citric acid pH 4.6, 7% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.65 53.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.57 α = 90 b = 80.57 β = 90 c = 209.966 γ = 90
Symmetry Space Group P 43 21 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 PIXEL DECTRIS PILATUS3 S 6M 2018-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.988 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 50 99.8 26.1 13.4 47534
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.04 99.4 0.344 1.6 10.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2AW5 2.31 40.32 29682 1576 99.35 0.19973 0.19743 0.24389 0.2067 RANDOM 66.799
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] 3.04 3.04 -6.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.869 r_dihedral_angle_4_deg 17.963 r_dihedral_angle_3_deg 15.241 r_long_range_B_other 10.821 r_long_range_B_refined 10.812 r_scangle_other 8.166 r_mcangle_it 7.48 r_mcangle_other 7.479 r_dihedral_angle_1_deg 6.141 r_scbond_it 5.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.869 r_dihedral_angle_4_deg 17.963 r_dihedral_angle_3_deg 15.241 r_long_range_B_other 10.821 r_long_range_B_refined 10.812 r_scangle_other 8.166 r_mcangle_it 7.48 r_mcangle_other 7.479 r_dihedral_angle_1_deg 6.141 r_scbond_it 5.529 r_scbond_other 5.526 r_mcbond_it 5.196 r_mcbond_other 5.195 r_angle_refined_deg 1.574 r_angle_other_deg 0.85 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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 4377 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing