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Crystal structure of OpuBC in complex with DMSP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5 273 150 to 225 mM potassium acetate and 20% to 27.5% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.81 32.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.77 α = 90 b = 65.89 β = 92.14 c = 63.58 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 MAR CCD 130 mm 2015-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 1.6 63.5 99.88 0.083 12.4 4.9 32423
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 1.6 1.66 99.9 0.39 4.7 4.7
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 3R6U 1.6 63.5 30871 1563 99.88 0.1713 0.16927 0.1676 0.20983 0.2084 RANDOM 16.038
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] 0.12 0.14 0.44 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.026 r_dihedral_angle_4_deg 22.417 r_dihedral_angle_3_deg 15.348 r_dihedral_angle_1_deg 6.282 r_angle_refined_deg 2.05 r_chiral_restr 0.151 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.026 r_dihedral_angle_4_deg 22.417 r_dihedral_angle_3_deg 15.348 r_dihedral_angle_1_deg 6.282 r_angle_refined_deg 2.05 r_chiral_restr 0.151 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 2221 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing