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Crystal structure of the yfdW gene product of E. coli, in complex with oxalate and acetyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PT7 Apo-form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 PEG600, cacodylate,oxalate, acethylCoA , pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.17 70.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.786 α = 90 b = 146.786 β = 90 c = 129.905 γ = 120
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 210 mirrors 2003-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979257 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 20 98.7 0.114 3.9 4 79388 79388 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 98.3 0.234 3 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 Apo-form 2.2 20 79388 72739 6647 98.8 0.1825 0.18251 0.18056 0.183 0.2037 0.206 RANDOM 41.451
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] -1.65 -0.83 -1.65 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.032 r_scangle_it 4.162 r_scbond_it 2.669 r_angle_refined_deg 1.623 r_mcangle_it 1.559 r_mcbond_it 0.848 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.186 r_symmetry_vdw_refined 0.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.032 r_scangle_it 4.162 r_scbond_it 2.669 r_angle_refined_deg 1.623 r_mcangle_it 1.559 r_mcbond_it 0.848 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.186 r_symmetry_vdw_refined 0.179 r_chiral_restr 0.101 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6440 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling AMoRE phasing