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Crystal structure of the maize chloroplastic non-photosynthetic NADP(+)-dependent malic enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 8% w/v PEG20000, 8% w/v PEG550 MME, 50 mM Tris-HCl, pH 8.5, 1.2 M sodium formate
Crystal Properties Matthews coefficient Solvent content 3.26 62.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.453 α = 90 b = 108.115 β = 90 c = 168.952 γ = 90
Symmetry Space Group P 21 2 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 2024-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 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 2.55 91.232 99.9 0.112 0.122 0.049 0.998 9.7 6 55927 65
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 2.55 2.62 100 1.832 2.003 0.803 0.603 1 6.2
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 (All) 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 2.55 91.232 55877 2736 99.846 0.247 0.2467 0.2435 0.256 0.3083 0.3225 RANDOM 103
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] -3.608 11.419 -7.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.551 r_dihedral_angle_3_deg 20.696 r_dihedral_angle_4_deg 19.643 r_lrange_it 17.728 r_lrange_other 17.727 r_mcangle_it 13.688 r_mcangle_other 13.687 r_scangle_it 12.614 r_scangle_other 12.613 r_mcbond_it 9.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.551 r_dihedral_angle_3_deg 20.696 r_dihedral_angle_4_deg 19.643 r_lrange_it 17.728 r_lrange_other 17.727 r_mcangle_it 13.688 r_mcangle_other 13.687 r_scangle_it 12.614 r_scangle_other 12.613 r_mcbond_it 9.107 r_mcbond_other 9.106 r_scbond_it 8.061 r_scbond_other 8.06 r_dihedral_angle_1_deg 8.016 r_angle_refined_deg 1.753 r_angle_other_deg 1.214 r_nbd_other 0.275 r_nbd_refined 0.244 r_symmetry_nbd_refined 0.218 r_symmetry_nbd_other 0.206 r_xyhbond_nbd_refined 0.201 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.161 r_ncsr_local_group_1 0.16 r_metal_ion_refined 0.102 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8316 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction Aimless data scaling BALBES phasing