2YLN

Crystal structure of the L-cystine solute receptor of Neisseria gonorrhoeae in the closed conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZSFPDB ENTRY 3ZSF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
141.6 M AMMONIUM SULFATE, 100 MM NA-CITRATE PH 4.0.
Crystal Properties
Matthews coefficientSolvent content
1.379.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.73α = 90
b = 63.43β = 96.89
c = 44.65γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.1230.96990.0616.33.875069-37.42
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.121.1590.70.542.32.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3ZSF1.1230.967131437541000.110870.109230.14176RANDOM8.232
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]
-0.31-0.270.32-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.99
r_dihedral_angle_4_deg25.197
r_dihedral_angle_3_deg12.279
r_scangle_it7.305
r_dihedral_angle_1_deg7.185
r_scbond_it5.048
r_mcangle_it3.031
r_mcbond_it2.185
r_angle_refined_deg2.137
r_rigid_bond_restr2.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.99
r_dihedral_angle_4_deg25.197
r_dihedral_angle_3_deg12.279
r_scangle_it7.305
r_dihedral_angle_1_deg7.185
r_scbond_it5.048
r_mcangle_it3.031
r_mcbond_it2.185
r_angle_refined_deg2.137
r_rigid_bond_restr2.078
r_angle_other_deg1.067
r_mcbond_other0.772
r_chiral_restr0.12
r_bond_refined_d0.023
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms1806
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing