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Crystal structure of rhamnogalacturonan lyase YesW complexed with rhamnose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z8R PDB ENTRY 2Z8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.4 293 55% MPD, 0.1M TRIS, pH8.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.282 α = 90 b = 105.858 β = 94.82 c = 100.967 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 RIGAKU JUPITER 210 mirror 2008-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.8000 SPring-8 BL38B1
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 1.32 50 97.6 0.066 13 3.8 280440
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) 1.32 1.37 95.1 0.338 2.8 3.6
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 2Z8R 1.32 50 259908 13803 97.39 0.16704 0.16633 0.1655 0.18033 0.1801 RANDOM 16.536
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] 0.1 0.52 0.74 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_4_deg 17.449 r_dihedral_angle_3_deg 11.393 r_dihedral_angle_1_deg 6.497 r_scangle_it 1.915 r_scbond_it 1.326 r_angle_refined_deg 1.166 r_mcangle_it 0.882 r_mcbond_it 0.547 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_4_deg 17.449 r_dihedral_angle_3_deg 11.393 r_dihedral_angle_1_deg 6.497 r_scangle_it 1.915 r_scbond_it 1.326 r_angle_refined_deg 1.166 r_mcangle_it 0.882 r_mcbond_it 0.547 r_nbtor_refined 0.307 r_nbd_refined 0.197 r_metal_ion_refined 0.153 r_symmetry_vdw_refined 0.137 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.079 r_xyhbond_nbd_refined 0.077 r_symmetry_metal_ion_refined 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8954 Nucleic Acid Atoms Solvent Atoms 1271 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing