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Human malic enzyme 3 complex with inhibitor NPD-389 at 1.82 Angstrom.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In lab model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2 M Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris propane pH: 8.5, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.624 α = 90 b = 60.275 β = 90.81 c = 159.501 γ = 90
Symmetry Space Group I 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 2023-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 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 1.82 45.483 99 0.988 6.1 3.6 114678
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 1.82 1.85 0.428 0.6
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.82 45.483 114636 5892 98.984 0.19 0.1894 0.1976 0.2075 0.2134 27.829
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] -1.468 0.709 0.212 1.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.901 r_dihedral_angle_3_deg 12.085 r_dihedral_angle_1_deg 5.52 r_dihedral_angle_2_deg 5.452 r_lrange_it 4.572 r_lrange_other 4.384 r_scangle_it 2.765 r_scangle_other 2.765 r_mcangle_it 2.052 r_mcangle_other 2.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.901 r_dihedral_angle_3_deg 12.085 r_dihedral_angle_1_deg 5.52 r_dihedral_angle_2_deg 5.452 r_lrange_it 4.572 r_lrange_other 4.384 r_scangle_it 2.765 r_scangle_other 2.765 r_mcangle_it 2.052 r_mcangle_other 2.052 r_scbond_it 1.606 r_scbond_other 1.606 r_mcbond_it 1.22 r_mcbond_other 1.219 r_angle_refined_deg 1.017 r_dihedral_angle_other_2_deg 0.78 r_angle_other_deg 0.378 r_nbd_refined 0.202 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.111 r_symmetry_xyhbond_nbd_refined 0.111 r_nbd_other 0.11 r_symmetry_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.051 r_chiral_restr_other 0.004 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8666 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 190
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing