4YGJ | pdb_00004ygj

NaBr--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
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.299α = 90
b = 41.379β = 104.64
c = 72.46γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-08-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.0NSLSX25

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
11.025094.1341.71.388157
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.021.041.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTPDB entry 3RYY1.15088157457694.130.128120.127140.130.146750.15RANDOM14.148
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]
0.18-0.06-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.5
r_dihedral_angle_4_deg28.887
r_sphericity_free19.467
r_dihedral_angle_3_deg11.477
r_rigid_bond_restr7.389
r_sphericity_bonded6.748
r_dihedral_angle_1_deg6.742
r_long_range_B_refined2.876
r_scbond_it2.863
r_scbond_other2.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.5
r_dihedral_angle_4_deg28.887
r_sphericity_free19.467
r_dihedral_angle_3_deg11.477
r_rigid_bond_restr7.389
r_sphericity_bonded6.748
r_dihedral_angle_1_deg6.742
r_long_range_B_refined2.876
r_scbond_it2.863
r_scbond_other2.862
r_scangle_other2.801
r_long_range_B_other2.718
r_angle_refined_deg2.351
r_mcangle_other1.654
r_mcangle_it1.647
r_mcbond_it1.37
r_mcbond_other1.367
r_angle_other_deg1.06
r_chiral_restr0.159
r_bond_refined_d0.024
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 Atoms2044
Nucleic Acid Atoms
Solvent Atoms269
Heterogen Atoms11

Software

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