3EQM | pdb_00003eqm

Crystal structure of human placental aromatase cytochrome P450 in complex with androstenedione

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.4	277	Freshly purified aromatase in 100mM potassium phosphate buffer, pH 7.4, containing 20% glycerol, 0.1mM androstenedione, and 1mM n-dodecyl-D-maltopyranoside (BDM) was mixed with reservoir cocktails of 24 to 30% polyethylene glycol 4000 and 0.5M NaCl in 0.05M Tris-HCl buffer pH 8.5 and vapor diffused in sealed 24-well sitting drop plates against corresponding reservoir solution. The purification and crystallization experiments were all conducted at 4 C. Reddish-brown color hexagonal rod-shaped crystals appeared in 7-10 days and continued to grow up to 14-16 days, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
5.84	78.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.208	α = 90
b = 140.208	β = 90
c = 119.266	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 315		2007-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979	APS	19-ID

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	2.897	121.27	99.51			30371	28808

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	2.897	2.972	99.6		0.067	31.1	6.1	30371

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.9	37.77	30371	28808	1532	99.39	0.21526	0.21372	0.2115	0.24439	0.2398	RANDOM	77.281

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]
2.89	1.44		2.89		-4.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.69
r_dihedral_angle_3_deg	20.152
r_dihedral_angle_4_deg	14.316
r_dihedral_angle_1_deg	6.14
r_scangle_it	1.712
r_angle_refined_deg	1.321
r_scbond_it	1.007
r_mcangle_it	0.88
r_mcbond_it	0.472
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.102
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3658
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	74

Software

Software
Software Name	Purpose
HKL-3000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling