☰ Navigation Tabs
Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution
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 2.36 47.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.897 α = 90 b = 106.153 β = 95.11 c = 101.041 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 2006-03-08 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 1.4 50 97.2 0.052 10.5 3.3 233253 11.8
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) 1.4 1.45 86.7 0.398 1.49 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.4 28.4 217773 11499 98.22 0.16445 0.16351 0.1642 0.18215 0.1833 RANDOM 15.348
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.058 r_dihedral_angle_4_deg 18.652 r_dihedral_angle_3_deg 11.883 r_dihedral_angle_1_deg 6.227 r_scangle_it 1.832 r_scbond_it 1.293 r_angle_refined_deg 1.18 r_mcangle_it 0.836 r_mcbond_it 0.505 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.058 r_dihedral_angle_4_deg 18.652 r_dihedral_angle_3_deg 11.883 r_dihedral_angle_1_deg 6.227 r_scangle_it 1.832 r_scbond_it 1.293 r_angle_refined_deg 1.18 r_mcangle_it 0.836 r_mcbond_it 0.505 r_nbtor_refined 0.305 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.149 r_metal_ion_refined 0.145 r_symmetry_hbond_refined 0.109 r_xyhbond_nbd_refined 0.087 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9684 Nucleic Acid Atoms Solvent Atoms 1409 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing