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Crystal structure of rhamnogalacturonan lyase YesW complexed with digalacturonic acid
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 293.0K
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.617 α = 90 b = 105.152 β = 95.22 c = 100.668 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 277 AREA DETECTOR SIEMENS HI-STAR 2007-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE MACSCIENCE
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 2.5 26.2 93.3 0.059 12.4 1.53 37253 18
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) 2.5 2.59 70 0.233 2.41 1.14
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 2.5 26.15 31603 1708 81.91 0.16568 0.16157 0.1624 0.24169 0.2406 RANDOM 21.003
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.5 r_dihedral_angle_4_deg 18.889 r_dihedral_angle_3_deg 16.502 r_dihedral_angle_1_deg 6.71 r_scangle_it 1.434 r_angle_refined_deg 1.259 r_scbond_it 0.893 r_mcangle_it 0.734 r_mcbond_it 0.415 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.5 r_dihedral_angle_4_deg 18.889 r_dihedral_angle_3_deg 16.502 r_dihedral_angle_1_deg 6.71 r_scangle_it 1.434 r_angle_refined_deg 1.259 r_scbond_it 0.893 r_mcangle_it 0.734 r_mcbond_it 0.415 r_nbtor_refined 0.315 r_symmetry_hbond_refined 0.256 r_nbd_refined 0.224 r_metal_ion_refined 0.22 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8952 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement SADIE data collection SAINT data reduction SAINT data scaling MOLREP phasing