3TBG | pdb_00003tbg

Human cytochrome P450 2D6 with two thioridazines bound in active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QM4	PDB ENTRY 3QM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	PEG3350, sodium acetate, sodium cacodylate, potassium phosphate, sodium chloride, zinc chloride, glycerol, beta-mercaptoethanol, thioridazine, HEGA-10, facial amphiphile 231_CHOL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.19	α = 90
b = 191.96	β = 90
c = 249.48	γ = 90

Symmetry
Space Group	P 21 21 21

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	Rh coated flat mirror	2011-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97945	SSRL	BL7-1

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	2.04	37.957	99.8	0.088	0.088	4.8	3.9	174928	174399			24.036

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.04	2.15	100		0.352	0.352	1.5	4	25169

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB ENTRY 3QM4	2.1	36.9	161318	160415	8054	99.5	0.222	0.222	0.21	0.247	0.24	RANDOM	34.8

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]
-2.76			-6.91		9.67

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.1
c_scangle_it	3.02
c_scbond_it	2.08
c_mcangle_it	2.04
c_mcbond_it	1.31
c_angle_deg	1.2
c_improper_angle_d	0.79
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14608
Nucleic Acid Atoms
Solvent Atoms	504
Heterogen Atoms	426

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling