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Crystal structure of the binding protein OpuAC in complex with glycine betaine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Selenomethionine derivative
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.25 274 Tris, ammonium acetate, PEG 4000, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 274K
Crystal Properties Matthews coefficient Solvent content 2.13 42.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.818 α = 90 b = 88.486 β = 90 c = 95.714 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.05 MPG/DESY, HAMBURG BW6
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 1.98 17 98.9 0.111 19295 18948 2
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 1.98 2.02 99 0.286 6 895
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 (All) 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 Selenomethionine derivative 2 17 16355 886 96.52 0.20392 0.20125 0.2227 0.2552 0.2164 RANDOM 31.537
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] 1.32 0.06 -1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.834 r_dihedral_angle_3_deg 16.422 r_dihedral_angle_4_deg 10.358 r_dihedral_angle_1_deg 8.582 r_scangle_it 1.819 r_scbond_it 1.192 r_angle_refined_deg 1.129 r_angle_other_deg 0.778 r_mcangle_it 0.632 r_xyhbond_nbd_refined 0.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.834 r_dihedral_angle_3_deg 16.422 r_dihedral_angle_4_deg 10.358 r_dihedral_angle_1_deg 8.582 r_scangle_it 1.819 r_scbond_it 1.192 r_angle_refined_deg 1.129 r_angle_other_deg 0.778 r_mcangle_it 0.632 r_xyhbond_nbd_refined 0.605 r_mcbond_it 0.502 r_symmetry_hbond_refined 0.317 r_nbd_refined 0.197 r_nbd_other 0.17 r_symmetry_vdw_other 0.153 r_symmetry_vdw_refined 0.12 r_xyhbond_nbd_other 0.093 r_mcbond_other 0.089 r_nbtor_other 0.085 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2091 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing