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Crystal Structure of Xylobiose-BxlE complex from Streptomyces thermoviolaceus OPC-520
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.2 293 25% PEG 3350, 0.1M citrate, 15% glycerol, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.94 36.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.672 α = 90 b = 163.157 β = 90 c = 42.931 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII M MAD 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU SPring-8 BL41XU 2 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 1,2 1.78 45 98.1 0.071 70761 69417 2 1
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 MAD THROUGHOUT 1.85 33.81 59174 3111 98.46 0.17026 0.16802 0.1689 0.21282 0.2125 RANDOM 15.681
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 36.694 r_dihedral_angle_4_deg 16.699 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 6.117 r_scangle_it 5.394 r_scbond_it 3.548 r_mcangle_it 2.009 r_angle_refined_deg 1.816 r_mcbond_it 1.171 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.694 r_dihedral_angle_4_deg 16.699 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 6.117 r_scangle_it 5.394 r_scbond_it 3.548 r_mcangle_it 2.009 r_angle_refined_deg 1.816 r_mcbond_it 1.171 r_chiral_restr 0.134 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6074 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement