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Human malic enzyme 2 complex with inhibitor NPD-389
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 0.1 M SPG (Succinic acid, Sodium phosphate monobasic monohydrate, Glycine), 25% PEG-1500, pH= 6.0.
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.048 α = 90 b = 58.923 β = 101.938 c = 106.929 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER X 16M 2023-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.45 49.219 100 0.998 9 12 46166 51.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 100 0.595 0.9
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.45 49.219 46162 2378 99.95 0.232 0.2294 0.2368 0.278 0.2827 Random selection 66.906
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] -7.235 -1.707 7.747 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.082 r_dihedral_angle_6_deg 11.912 r_lrange_it 6.136 r_lrange_other 6.136 r_dihedral_angle_1_deg 5.649 r_dihedral_angle_2_deg 4.022 r_scangle_it 3.958 r_scangle_other 3.958 r_mcangle_it 3.794 r_mcangle_other 3.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.082 r_dihedral_angle_6_deg 11.912 r_lrange_it 6.136 r_lrange_other 6.136 r_dihedral_angle_1_deg 5.649 r_dihedral_angle_2_deg 4.022 r_scangle_it 3.958 r_scangle_other 3.958 r_mcangle_it 3.794 r_mcangle_other 3.794 r_scbond_it 2.277 r_scbond_other 2.276 r_mcbond_it 2.265 r_mcbond_other 2.263 r_angle_refined_deg 0.896 r_dihedral_angle_other_2_deg 0.837 r_angle_other_deg 0.322 r_nbd_refined 0.196 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.136 r_nbd_other 0.108 r_symmetry_nbd_refined 0.083 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_refined 0.05 r_chiral_restr 0.041 r_symmetry_xyhbond_nbd_other 0.004 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_chiral_restr_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8679 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 243
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing