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Crystal structure of lactococcal OpuAC in its closed-liganded conformation complexed with glycine betaine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3L6G PDB code 3L6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2 M NaCl, 0.1 M Na-Hepes, pH 7.0, 20% PEG 6000, 1 mM glycine betaine, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.19 61.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.706 α = 90 b = 111.706 β = 90 c = 151.728 γ = 120
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 MARMOSAIC 225 mm CCD 2009-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.872 ESRF ID23-2
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 2.2 46 97.4 0.114 10.71 16390 2 34.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.33 96.1 0.666 2.5
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 MOLECULAR REPLACEMENT THROUGHOUT PDB code 3L6G 2.3 40.78 16379 15560 819 100 0.19843 0.1972 0.191 0.22137 0.2067 RANDOM 19.832
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] -1.05 -0.53 -1.05 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.819 r_dihedral_angle_3_deg 11.858 r_dihedral_angle_4_deg 9.882 r_dihedral_angle_1_deg 4.907 r_scangle_it 1.165 r_angle_refined_deg 0.898 r_angle_other_deg 0.778 r_scbond_it 0.7 r_mcangle_it 0.438 r_mcbond_it 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.819 r_dihedral_angle_3_deg 11.858 r_dihedral_angle_4_deg 9.882 r_dihedral_angle_1_deg 4.907 r_scangle_it 1.165 r_angle_refined_deg 0.898 r_angle_other_deg 0.778 r_scbond_it 0.7 r_mcangle_it 0.438 r_mcbond_it 0.22 r_chiral_restr 0.052 r_mcbond_other 0.032 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1995 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 10
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction