5DBY | pdb_00005dby

Crystal Structure of Equine Serum Albumin in Complex with Diclofenac and Naproxen Obtained in Displacement Experiment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OT2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	2.0 M ammonium sulfate, 0.1 M acetate buffer pH 5.0, unliganded crystal was soaked in the diclofenac solution for 1h and transferred to the naproxen solution for 1h

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.32	α = 90
b = 94.32	β = 90
c = 141.69	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300-HS		2015-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.35	50	99.9	0.077	15.37	5.09	29716	29700		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.45	100		0.989	2.03	5.1

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4OT2	2.35	50.01	28576	1121	99.93	0.19499	0.19332	0.2	0.23397	0.24	RANDOM	58.944

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]
-0.39	-0.19		-0.39		1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.852
r_dihedral_angle_3_deg	18.672
r_dihedral_angle_4_deg	17.336
r_dihedral_angle_1_deg	6.911
r_long_range_B_refined	5.806
r_long_range_B_other	5.804
r_angle_refined_deg	1.93
r_scangle_other	1.463
r_angle_other_deg	1.135
r_scbond_it	1.045
r_scbond_other	1.045
r_mcangle_it	0.897
r_mcangle_other	0.897
r_mcbond_it	0.602
r_mcbond_other	0.602
r_chiral_restr	0.108
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.003
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 Atoms	Number
Protein Atoms	4568
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	phasing
XSCALE	data scaling
XDS	data reduction