3APV

Crystal structure of the A variant of human alpha1-acid glycoprotein and amitriptyline complex

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	30% PEG 4000, 0.2M ammonium sulfate, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.65	α = 90
b = 45.948	β = 92.14
c = 120.732	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315r		2009-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.15	50	98.8	0.059	0.524			20082	20082

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)
	2.15	2.23	93.8		0.177	8.1

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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3APU	2.15	36.31	18955	971	98.86	0.22183	0.21947	0.26712	RANDOM	50.721

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]
0.05		-0.07	0.07		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.816
r_dihedral_angle_3_deg	17.484
r_dihedral_angle_4_deg	13.188
r_dihedral_angle_1_deg	6.836
r_scangle_it	2.682
r_scbond_it	1.635
r_angle_refined_deg	1.445
r_mcangle_it	1.086
r_mcbond_it	0.582
r_chiral_restr	0.098
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2869
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	46

Software

Software
Software Name	Purpose
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing