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Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme in a pentary complex with natural substrate malate, ATP, Mn++, and allosteric activator fumarate.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 100 mM MES (pH6.0), 10% PEG 20,000, 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.73 54.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 226.05 α = 90 b = 117.345 β = 109 c = 111.31 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 CCD ADSC QUANTUM 4 2000-12-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 0.9876 APS 32-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.3 30 97.6 0.086 0.086 119748 119648 24.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.38 94.2 0.21
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) 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 2.3 19.94 2 2 119748 112845 8496 92.7 0.22 0.211 0.211 0.217 0.252 0.2581 RANDOM 30.8
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] 6.05 -0.07 -3.42 -2.63
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.3 c_scangle_it 3.03 c_scbond_it 2.09 c_mcangle_it 1.92 c_angle_deg 1.3 c_mcbond_it 1.2 c_improper_angle_d 0.84 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17436 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms 320
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling COMO phasing