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Crystal structure of the G200R mutant from the maize chloroplastic photosynthetic NADP(+)-dependent malic enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 277 2.0 M ammonium sulfate, 0.1 M sodium acetate/acetic acid buffer, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.679 α = 90 b = 124.161 β = 90 c = 189.472 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 PIXEL DECTRIS EIGER X 16M 2024-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97623 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.7 124.16 99.1 0.19 0.213 0.092 0.993 5.3 5.3 63889 50
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.77 99.8 1.687 1.865 0.78 0.62 1.1 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.7 50.01 60592 3227 98.74 0.24182 0.23895 0.2522 0.29617 0.3023 RANDOM 61.416
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] -6.49 9.77 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.281 r_dihedral_angle_4_deg 21.383 r_dihedral_angle_3_deg 20.407 r_long_range_B_refined 13.761 r_long_range_B_other 13.761 r_scangle_other 10.743 r_mcangle_it 9.279 r_mcangle_other 9.278 r_scbond_it 7.119 r_scbond_other 7.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.281 r_dihedral_angle_4_deg 21.383 r_dihedral_angle_3_deg 20.407 r_long_range_B_refined 13.761 r_long_range_B_other 13.761 r_scangle_other 10.743 r_mcangle_it 9.279 r_mcangle_other 9.278 r_scbond_it 7.119 r_scbond_other 7.119 r_dihedral_angle_1_deg 6.981 r_mcbond_it 6.33 r_mcbond_other 6.33 r_angle_refined_deg 1.707 r_angle_other_deg 1.253 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 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 17433 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction Aimless data scaling MrBUMP phasing