4YGK

NaSCN--Interactions between Hofmeister Anions and the Binding Pocket of a Protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RYYPDB entry 3RYY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.8277100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.1342.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.391α = 90
b = 41.346β = 104.7
c = 72.912γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.55095.919.62.737916
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5386.12.1

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 DIFFRACTIONTHROUGHOUTPDB entry 3RYY1.55035994190695.820.175350.173370.21335RANDOM10.01
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]
-0.1-0.03-0.040.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.576
r_dihedral_angle_4_deg28.787
r_dihedral_angle_3_deg12.609
r_dihedral_angle_1_deg6.892
r_long_range_B_refined3.846
r_long_range_B_other3.738
r_scangle_other2.837
r_angle_refined_deg2.115
r_scbond_it1.916
r_scbond_other1.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.576
r_dihedral_angle_4_deg28.787
r_dihedral_angle_3_deg12.609
r_dihedral_angle_1_deg6.892
r_long_range_B_refined3.846
r_long_range_B_other3.738
r_scangle_other2.837
r_angle_refined_deg2.115
r_scbond_it1.916
r_scbond_other1.914
r_mcangle_other1.91
r_mcangle_it1.908
r_mcbond_it1.252
r_mcbond_other1.244
r_angle_other_deg1.024
r_chiral_restr0.163
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2049
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling