☰ Navigation Tabs
Crystal structure of CqsB2 from Streptomyces exfoliatus in complex with the product, 1-(2-hydroxypropyl)-2-methyl-carbazole-3,4-dione
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris-HCl (pH8.5), 30% (w/v) PEG 4000, 0.2M LiSO4
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.227 α = 90 b = 128.227 β = 90 c = 125.431 γ = 90
Symmetry Space Group P 4 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 PIXEL DECTRIS PILATUS3 2M 2017-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.1 125.43 100 0.132 0.035 0.994 24 14.7 61403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 0.543 0.145 0.948
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 6IPV 2.1 125.43 58471 2903 99.93 0.18009 0.17794 0.1864 0.22389 0.2283 RANDOM 24.664
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.184 r_dihedral_angle_4_deg 16.364 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_1_deg 6.821 r_long_range_B_refined 5.109 r_long_range_B_other 5.088 r_scangle_other 2.758 r_mcangle_it 2.16 r_mcangle_other 2.16 r_scbond_it 1.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.184 r_dihedral_angle_4_deg 16.364 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_1_deg 6.821 r_long_range_B_refined 5.109 r_long_range_B_other 5.088 r_scangle_other 2.758 r_mcangle_it 2.16 r_mcangle_other 2.16 r_scbond_it 1.676 r_scbond_other 1.676 r_angle_refined_deg 1.346 r_mcbond_it 1.345 r_mcbond_other 1.341 r_angle_other_deg 0.802 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7212 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing