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Crystal structure of the L-cystine solute receptor of Neisseria gonorrhoeae in the closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZSF PDB ENTRY 3ZSF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 1.6 M AMMONIUM SULFATE, 100 MM NA-CITRATE PH 4.0.
Crystal Properties Matthews coefficient Solvent content 1.37 9.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.73 α = 90 b = 63.43 β = 96.89 c = 44.65 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 MARMOSAIC 225 mm CCD 2010-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 1.12 30.96 99 0.06 16.3 3.8 75069 -3 7.42
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) 1 1.12 1.15 90.7 0.54 2.3 2.7
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 PDB ENTRY 3ZSF 1.12 30.96 71314 3754 100 0.11087 0.10923 0.1207 0.14176 0.1505 RANDOM 8.232
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] -0.31 -0.27 0.32 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.99 r_dihedral_angle_4_deg 25.197 r_dihedral_angle_3_deg 12.279 r_scangle_it 7.305 r_dihedral_angle_1_deg 7.185 r_scbond_it 5.048 r_mcangle_it 3.031 r_mcbond_it 2.185 r_angle_refined_deg 2.137 r_rigid_bond_restr 2.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.99 r_dihedral_angle_4_deg 25.197 r_dihedral_angle_3_deg 12.279 r_scangle_it 7.305 r_dihedral_angle_1_deg 7.185 r_scbond_it 5.048 r_mcangle_it 3.031 r_mcbond_it 2.185 r_angle_refined_deg 2.137 r_rigid_bond_restr 2.078 r_angle_other_deg 1.067 r_mcbond_other 0.772 r_chiral_restr 0.12 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 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_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1806 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing