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Human malic enzyme 2 complex with FLA at 2 Angstrom.
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 293 0.2 M Ammonium citrate dibasic, 20% PEG-3350. (JCSG A3)
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.223 α = 90 b = 59.502 β = 102.087 c = 106.595 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 2024-08-09 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 49.22 100 0.999 12.3 28 84951
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 2.04 98.9 0.853 1.4
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 2 49.268 84895 4294 99.923 0.204 0.2031 0.2169 0.2141 0.2308 RANDOM 46.865
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] -4.988 -0.172 5.114 -0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.202 r_dihedral_angle_3_deg 12.957 r_dihedral_angle_1_deg 5.828 r_dihedral_angle_2_deg 4.239 r_dihedral_angle_other_2_deg 1.253 r_angle_refined_deg 1.037 r_angle_other_deg 0.383 r_nbd_refined 0.209 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.202 r_dihedral_angle_3_deg 12.957 r_dihedral_angle_1_deg 5.828 r_dihedral_angle_2_deg 4.239 r_dihedral_angle_other_2_deg 1.253 r_angle_refined_deg 1.037 r_angle_other_deg 0.383 r_nbd_refined 0.209 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.179 r_nbd_other 0.135 r_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.107 r_symmetry_nbd_refined 0.099 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.051 r_symmetry_xyhbond_nbd_other 0.042 r_gen_planes_refined 0.004 r_bond_refined_d 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 8585 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing