6CI6 | pdb_00006ci6

Crystal structure of equine serum albumin in complex with nabumetone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V08

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	289	1 ul of 34 mg/ml protein in 10 mM Tris pH 7.4 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl, 2.2 M (NH4)2SO4 final pH 7.4) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen). Crystals were soaked with 10 mM nabumetone

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.879	α = 90
b = 93.879	β = 90
c = 140.787	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	PIXEL	DECTRIS PILATUS3 6M	1000 um thick sensor. Mirrors: adjustable focus K-B pair Si plus Pt, Rh coatings	2016-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97949	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.8	50.01	100	0.115	0.115	0.129	0.057	4.6	5.1		17321		-3	63.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.85	100		0.66	0.66	0.742	0.335	0.816		4.9

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3V08	2.8	50.01	16496	788	99.75	0.1858	0.1824	0.2557	0.2535	RANDOM	64.159

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]
1.69	0.84		1.69		-5.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.826
r_dihedral_angle_4_deg	15.27
r_dihedral_angle_3_deg	13.869
r_dihedral_angle_1_deg	4.837
r_angle_refined_deg	1.088
r_angle_other_deg	0.861
r_chiral_restr	0.055
r_bond_refined_d	0.007
r_bond_other_d	0.006
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4524
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
MOLREP	phasing
HKL-3000	phasing
PDB_EXTRACT	data extraction
SCALEPACK	data scaling