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Formyl-CoA transferase with aspartyl-CoA thioester intermediate derived from formyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5H PDB ENTRY 1P5H
Crystallization Crystal Properties Matthews coefficient Solvent content 2.76 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.765 α = 90 b = 151.765 β = 90 c = 100.082 γ = 90
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 CCD 2007-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2 56 98.3 0.11 8.7 3.1 75233 2
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 2.11 94.3 0.39 1.8 2.4
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 1P5H 2 30 71459 3765 98.2 0.199 0.197 0.1986 0.242 0.242 RANDOM 25.35
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] 0.07 0.07 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.239 r_dihedral_angle_4_deg 16.811 r_dihedral_angle_3_deg 13.3 r_dihedral_angle_1_deg 5.677 r_scangle_it 1.698 r_mcangle_it 1.574 r_mcbond_it 1.397 r_scbond_it 1.216 r_angle_refined_deg 1.075 r_angle_other_deg 0.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.239 r_dihedral_angle_4_deg 16.811 r_dihedral_angle_3_deg 13.3 r_dihedral_angle_1_deg 5.677 r_scangle_it 1.698 r_mcangle_it 1.574 r_mcbond_it 1.397 r_scbond_it 1.216 r_angle_refined_deg 1.075 r_angle_other_deg 0.855 r_nbd_refined 0.179 r_nbd_other 0.179 r_symmetry_vdw_refined 0.174 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_other 0.126 r_symmetry_hbond_refined 0.125 r_nbtor_other 0.081 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6624 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing