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The structure of mitochondrial PEPCK, Complex with Mn and GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FAG PDB Entry 2FAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 298 16% PEG6000, 0.1M HEPES, n-octanoylsucrose, GDP, MnCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.595 α = 64.23 b = 90.852 β = 73.74 c = 103.339 γ = 71.18
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV Blue osmic, confocal 2005-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.09 100 95.3 0.106 3.3 127447
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) 1 2.09 2.18 91.9 0.581 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 PDB Entry 2FAG 2.09 32.81 120981 6402 94.69 0.1891 0.18673 0.1865 0.23366 0.2331 RANDOM 16.194
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] 0.1 -0.18 -1.16 0.67 -0.48 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.062 r_dihedral_angle_4_deg 17.345 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 6.264 r_scangle_it 1.662 r_angle_refined_deg 1.305 r_scbond_it 1.017 r_mcangle_it 0.539 r_mcbond_it 0.368 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.062 r_dihedral_angle_4_deg 17.345 r_dihedral_angle_3_deg 15.063 r_dihedral_angle_1_deg 6.264 r_scangle_it 1.662 r_angle_refined_deg 1.305 r_scbond_it 1.017 r_mcangle_it 0.539 r_mcbond_it 0.368 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.181 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18901 Nucleic Acid Atoms Solvent Atoms 1450 Heterogen Atoms 219
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling CNS refinement DENZO data reduction PDB_EXTRACT data extraction HKL-2000 data reduction CNS phasing