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Crystal structure of Gpb in complex with QUERCETIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SYM pdb entry 3SYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 10mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.47 50.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.6 α = 90 b = 126.6 β = 90 c = 115.821 γ = 90
Symmetry Space Group P 43 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 293 CCD MAR CCD 165 mm 2013-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8 EMBL/DESY, HAMBURG X13
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 2.34 30 100 0.101 18 9.9 40399 40399 -3
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) 1 2.34 2.38 100 0.461 5 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT pdb entry 3SYM 2.34 29.23 38265 38265 2023 99.65 0.18196 0.17866 0.1855 0.24395 0.2496 RANDOM 30.332
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_4_deg 20.955 r_dihedral_angle_3_deg 17.341 r_dihedral_angle_1_deg 6.782 r_mcangle_it 3.393 r_scbond_it 2.85 r_mcbond_it 2.188 r_mcbond_other 2.184 r_angle_refined_deg 1.616 r_angle_other_deg 0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_4_deg 20.955 r_dihedral_angle_3_deg 17.341 r_dihedral_angle_1_deg 6.782 r_mcangle_it 3.393 r_scbond_it 2.85 r_mcbond_it 2.188 r_mcbond_other 2.184 r_angle_refined_deg 1.616 r_angle_other_deg 0.895 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6578 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 26
Software Software Software Name Purpose DNA data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing