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Crystal structure of gene yfdW of E. coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PT7 apo-enzyme
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 PEG600, cacodylate, acetylCoA, pH 6.5, VAPOR DIFFUSION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 4.16 70.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.882 α = 90 b = 146.882 β = 90 c = 129.515 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 4 2002-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9330 ESRF ID14-4
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 20 99 0.078 7 6.5 105732 105732 2 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) 2 2.11 97.5 0.265
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT apo-enzyme 2 20 2 105732 96936 8795 99.08 0.1592 0.1592 0.15769 0.17598 0.1773 RANDOM 23.857
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] -1.38 -0.69 -1.38 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.367 r_scangle_it 4.373 r_scbond_it 2.644 r_mcangle_it 1.535 r_angle_refined_deg 1.498 r_mcbond_it 0.785 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.367 r_scangle_it 4.373 r_scbond_it 2.644 r_mcangle_it 1.535 r_angle_refined_deg 1.498 r_mcbond_it 0.785 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.193 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6432 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling AMoRE phasing