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Human malic enzyme 3 complex with NADP+ at 1.88 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 7.5 291 0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH: 7.5, 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.232 α = 90 b = 118.136 β = 90 c = 152.087 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 2024-08-09 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 1.88 49.01 100 0.995 7.6 17.7 112376
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 1.88 1.91 0.528 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 THROUGHOUT 1.88 49.038 112317 5717 99.926 0.188 0.1862 0.1932 0.2141 0.2187 RANDOM 34.993
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] -0.542 -0.848 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.204 r_dihedral_angle_3_deg 11.667 r_lrange_it 5.518 r_lrange_other 5.365 r_dihedral_angle_1_deg 5.351 r_dihedral_angle_2_deg 4.445 r_scangle_it 3.313 r_scangle_other 3.313 r_mcangle_it 2.686 r_mcangle_other 2.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.204 r_dihedral_angle_3_deg 11.667 r_lrange_it 5.518 r_lrange_other 5.365 r_dihedral_angle_1_deg 5.351 r_dihedral_angle_2_deg 4.445 r_scangle_it 3.313 r_scangle_other 3.313 r_mcangle_it 2.686 r_mcangle_other 2.686 r_scbond_it 1.936 r_scbond_other 1.931 r_dihedral_angle_other_2_deg 1.684 r_mcbond_it 1.602 r_mcbond_other 1.601 r_angle_refined_deg 0.977 r_angle_other_deg 0.369 r_nbd_refined 0.2 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.174 r_nbd_other 0.139 r_xyhbond_nbd_refined 0.128 r_symmetry_nbd_refined 0.122 r_symmetry_xyhbond_nbd_refined 0.101 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.05 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 8737 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing