6LUQ | pdb_00006luq

Haloperidol bound D2 dopamine receptor structure inspired discovery of subtype selective ligands

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6CM4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	100 mM Tris/HCl pH 7.5, 150 mM sodium malonate, 30% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.433	α = 90
b = 72.82	β = 90
c = 150.269	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	80	PIXEL	DECTRIS PILATUS3 6M		2019-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1	SPring-8	BL41XU

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	3.1	50	93.1	0.2	7.3	4.1		10160

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	3.1	3.2			1.13

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6CM4	3.1	33.386	9858	468	93.114	0.216	0.2152	0.22	0.229	0.23	RANDOM	71.564

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]
1.871			1.617		-3.488

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.275
r_dihedral_angle_4_deg	17.462
r_dihedral_angle_3_deg	16.645
r_dihedral_angle_1_deg	5.592
r_chiral_restr_other	1.622
r_angle_refined_deg	1.275
r_angle_other_deg	0.601
r_nbd_other	0.223
r_nbd_refined	0.222
r_symmetry_nbd_other	0.2
r_symmetry_xyhbond_nbd_other	0.183
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.104
r_symmetry_nbtor_other	0.088
r_gen_planes_refined	0.052
r_chiral_restr	0.047
r_gen_planes_other	0.045
r_bond_refined_d	0.006
r_bond_other_d	0.003
r_ext_dist_refined_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3168
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	106

Software

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