4YGL | pdb_00004ygl

NaClO4--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
2.1141.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.138α = 90
b = 41.04β = 104.45
c = 72.878γ = 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
11.515098.234.56.237479
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.5489.3203.6

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 DIFFRACTIONTHROUGHOUT1.5139.9335595187098.240.189160.187830.20.213350.22RANDOM11.346
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]
-0.150.01-0.110.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.399
r_dihedral_angle_4_deg23.622
r_dihedral_angle_3_deg12.479
r_dihedral_angle_1_deg6.881
r_long_range_B_refined4.245
r_long_range_B_other4.145
r_scangle_other3.371
r_angle_refined_deg2.552
r_scbond_it2.329
r_scbond_other2.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.399
r_dihedral_angle_4_deg23.622
r_dihedral_angle_3_deg12.479
r_dihedral_angle_1_deg6.881
r_long_range_B_refined4.245
r_long_range_B_other4.145
r_scangle_other3.371
r_angle_refined_deg2.552
r_scbond_it2.329
r_scbond_other2.323
r_mcangle_it2.147
r_mcangle_other2.147
r_mcbond_other1.46
r_mcbond_it1.459
r_angle_other_deg1.089
r_chiral_restr0.296
r_bond_refined_d0.027
r_gen_planes_refined0.015
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 Atoms2044
Nucleic Acid Atoms
Solvent Atoms215
Heterogen Atoms17

Software

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