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Human malic enzyme 1 complex with NADP+ at 1.9 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 0.3M Magnesium chloride hexahydrate;
0.3M Calcium chloride dihydrate, 0.1 M Tris (base); 0.1 M BICINE, 25% v/v MPD; 25% PEG1000; 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.126 α = 90 b = 181.214 β = 104.838 c = 108.594 γ = 90
Symmetry Space Group P 1 21 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 1.91 47.901 100 0.999 10.2 14.2 202104
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 1.91 1.94 0.379 0.7
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 1.91 47.901 202040 10290 99.983 0.198 0.1965 0.2012 0.228 0.2306 49.758
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] 2.682 2.827 -2.047 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.575 r_dihedral_angle_3_deg 12.066 r_dihedral_angle_1_deg 5.465 r_lrange_it 5.419 r_lrange_other 5.371 r_dihedral_angle_2_deg 4.481 r_scangle_it 3.809 r_scangle_other 3.809 r_mcangle_it 2.956 r_mcangle_other 2.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.575 r_dihedral_angle_3_deg 12.066 r_dihedral_angle_1_deg 5.465 r_lrange_it 5.419 r_lrange_other 5.371 r_dihedral_angle_2_deg 4.481 r_scangle_it 3.809 r_scangle_other 3.809 r_mcangle_it 2.956 r_mcangle_other 2.956 r_scbond_it 2.284 r_scbond_other 2.284 r_mcbond_it 1.912 r_mcbond_other 1.912 r_angle_refined_deg 0.96 r_angle_other_deg 0.356 r_dihedral_angle_other_2_deg 0.281 r_symmetry_xyhbond_nbd_refined 0.221 r_symmetry_nbd_refined 0.198 r_nbd_refined 0.195 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.172 r_nbd_other 0.134 r_xyhbond_nbd_refined 0.125 r_symmetry_nbtor_other 0.073 r_metal_ion_refined 0.07 r_chiral_restr 0.048 r_symmetry_xyhbond_nbd_other 0.033 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 17516 Nucleic Acid Atoms Solvent Atoms 1150 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing