4RWD | pdb_00004rwd

XFEL structure of the human delta opioid receptor in complex with a bifunctional peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4N6H	PDB entry 4N6H, PDB entry 4EIY
experimental model	PDB	4EIY	PDB entry 4N6H, PDB entry 4EIY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6	293	0.1M MES pH 6.0, 10-180mM Lithium citrate, 30-32% (v/v) PEG400, Lipidic cubic phase, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.23	α = 90
b = 89.29	β = 92.3
c = 96.42	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	294	PIXEL	Cornell-SLAC Pixel Array Detector (CSPAD)		2014-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.6	SLAC LCLS	CXI

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	2.7	33.5	100	0.118	6	560		36838

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	2.7	2.8	100		0.879	1.3	209

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 (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 4N6H, PDB entry 4EIY	2.7	33.45	34699	1831	99.92	0.20973	0.20827	0.21	0.23803	0.24	RANDOM	64.361

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]
-1.77		0.2	-0.41		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.909
r_dihedral_angle_3_deg	15.357
r_dihedral_angle_4_deg	11.068
r_long_range_B_refined	5.074
r_long_range_B_other	5.074
r_dihedral_angle_1_deg	4.382
r_scangle_other	3.501
r_mcangle_it	3.152
r_mcangle_other	3.152
r_scbond_it	2.102
r_scbond_other	2.102
r_mcbond_it	1.939
r_mcbond_other	1.939
r_angle_refined_deg	1.002
r_angle_other_deg	0.848
r_chiral_restr	0.048
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6163
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	136

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling