4YGN | pdb_00004ygn

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


X-RAY DIFFRACTION

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
2.1342.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.341α = 90
b = 41.336β = 104.57
c = 72.837γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-06-11MSINGLE 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
11.235082.429.72.659438
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.2526.641.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.235059438316387.960.176940.175250.180.209370.21RANDOM14.768
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]
0.15-0.02-0.230.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.926
r_dihedral_angle_4_deg24.994
r_sphericity_free16.772
r_dihedral_angle_3_deg12.37
r_rigid_bond_restr9.615
r_sphericity_bonded8.363
r_dihedral_angle_1_deg6.764
r_scbond_it4.003
r_scbond_other4.002
r_scangle_other3.949
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.926
r_dihedral_angle_4_deg24.994
r_sphericity_free16.772
r_dihedral_angle_3_deg12.37
r_rigid_bond_restr9.615
r_sphericity_bonded8.363
r_dihedral_angle_1_deg6.764
r_scbond_it4.003
r_scbond_other4.002
r_scangle_other3.949
r_long_range_B_refined3.527
r_long_range_B_other3.509
r_mcangle_other2.427
r_mcangle_it2.399
r_angle_refined_deg2.164
r_mcbond_it2.125
r_mcbond_other1.994
r_angle_other_deg1.099
r_chiral_restr0.203
r_bond_refined_d0.022
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2039
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms6

Software

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