4GL7 | pdb_00004gl7

Structure of human placental aromatase complexed with designed inhibitor HDDG046 (compound 5)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	277	The enzyme-inhibitor complexes were prepared by the addition from 20mM stock solutions of compound 5 in PEG550 to 18 M (~1mg/ml) of aromatase, to give a final inhibitor concentration of 300 microM. The mixture was incubated overnight at 4 C in 100mM potassium phosphate buffer pH 7.4 containing 20% glycerol, 20mM dithiothreitol, 0.5 microM ASD and 1mM BDM. The complex was then concentrated to 25-30mg/ml using ultrafiltration. Protein was setup for crystallization using protein to cocktail ratios 2:1 and 3:1. The protein was mixed with reservoir cocktails of 24-30% polyethylene glycol 4000 in 50mM NaCl, 50mM Tris, pH 8.5 and vapor diffused in sealed 24-well sitting drop plates against corresponding reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
5.92	79.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.445	α = 90
b = 141.445	β = 90
c = 118.851	γ = 120

Symmetry
Space Group	P 32 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 210		2011-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.978	CHESS	A1

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	3.9	122.49	99.5	0.114	16.7	4.6	12126	12126	2	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	3.9	50	12126	12126	621	98.98	0.21615	0.2142	0.21	0.25407	0.24	RANDOM	147.468

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]
2.68	1.34		2.68		-4.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.509
r_dihedral_angle_3_deg	22.526
r_dihedral_angle_4_deg	17.36
r_dihedral_angle_1_deg	7.298
r_scangle_it	1.857
r_angle_refined_deg	1.474
r_mcangle_it	1.103
r_scbond_it	1.005
r_mcbond_it	0.586
r_chiral_restr	0.106
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3658
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	70

Software

Software
Software Name	Purpose
ADSC	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing