☰ Navigation Tabs
The structure of chicken mitochondrial PEPCK in complex with PEP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 19% PEG6000, 0.1M HEPES pH 7.4, N-OCTANOYL SUCROSE, hanging drop vapor diffusion, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.349 α = 90 b = 48.023 β = 111.39 c = 126.317 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 CCD ADSC QUANTUM 4 2004-05-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9 SSRL BL11-1
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 1.9 50 97.9 0.117 7.6 4.9 95642
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 1.9 1.97 95.8 0.596 4.5 9246
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 2FAF 1.9 35.09 95631 4789 97.8 0.163 0.161 0.1611 0.2 0.2003 RANDOM 20.794
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] -0.03 -0.02 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.752 r_dihedral_angle_4_deg 15.656 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_1_deg 5.78 r_scangle_it 2.21 r_scbond_it 1.399 r_angle_refined_deg 1.324 r_mcangle_it 0.768 r_mcbond_it 0.516 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.752 r_dihedral_angle_4_deg 15.656 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_1_deg 5.78 r_scangle_it 2.21 r_scbond_it 1.399 r_angle_refined_deg 1.324 r_mcangle_it 0.768 r_mcbond_it 0.516 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.23 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9315 Nucleic Acid Atoms Solvent Atoms 996 Heterogen Atoms 69
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction