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Formyl-CoA transferase with aspartyl-CoA thioester intermediate derived from oxalyl-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 2.71 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.906 α = 90 b = 151.906 β = 90 c = 99.504 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 56.08 99.2 0.11 10.1 3.6 75655 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 97.2 0.3 2.4 2.8
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 1.97 30 74942 3910 98.8 0.175 0.173 0.1749 0.214 0.2188 RANDOM 23.59
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] 0.12 0.12 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.394 r_dihedral_angle_4_deg 16.215 r_dihedral_angle_3_deg 13.479 r_dihedral_angle_1_deg 5.698 r_scangle_it 1.89 r_mcangle_it 1.601 r_mcbond_it 1.417 r_scbond_it 1.337 r_angle_refined_deg 1.116 r_angle_other_deg 0.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.394 r_dihedral_angle_4_deg 16.215 r_dihedral_angle_3_deg 13.479 r_dihedral_angle_1_deg 5.698 r_scangle_it 1.89 r_mcangle_it 1.601 r_mcbond_it 1.417 r_scbond_it 1.337 r_angle_refined_deg 1.116 r_angle_other_deg 0.886 r_nbd_refined 0.183 r_nbd_other 0.182 r_symmetry_vdw_other 0.179 r_nbtor_refined 0.168 r_symmetry_vdw_refined 0.139 r_xyhbond_nbd_refined 0.133 r_symmetry_hbond_refined 0.123 r_nbtor_other 0.082 r_chiral_restr 0.072 r_bond_refined_d 0.008 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 787 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing