4YGJ

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RYY	PDB entry 3RYY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	277	100 mM Tris-Cl, 1.15 M sodium citrate, pH 7.8

Crystal Properties
Matthews coefficient	Solvent content
2.12	42

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.0	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.02	50	94.13	41.7	1.3		88157

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.02	1.04				1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB entry 3RYY	1.1	50	88157	4576	94.13	0.12812	0.12714	0.14675	RANDOM	14.148

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.5
r_dihedral_angle_4_deg	28.887
r_sphericity_free	19.467
r_dihedral_angle_3_deg	11.477
r_rigid_bond_restr	7.389
r_sphericity_bonded	6.748
r_dihedral_angle_1_deg	6.742
r_long_range_B_refined	2.876
r_scbond_it	2.863
r_scbond_other	2.862
r_scangle_other	2.801
r_long_range_B_other	2.718
r_angle_refined_deg	2.351
r_mcangle_other	1.654
r_mcangle_it	1.647
r_mcbond_it	1.37
r_mcbond_other	1.367
r_angle_other_deg	1.06
r_chiral_restr	0.159
r_bond_refined_d	0.024
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	2044
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling