6LI2

Crystal structure of GPR52 ligand free form with rubredoxin fusion

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model		Rosetta modelling

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE		293	0.08-0.1 M magnesium sulphate, 0.1 M sodium cacodylate trihydrate pH 6.2, and 28-31% PEG300

Crystal Properties
Matthews coefficient	Solvent content
3.83	67.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.223	α = 90
b = 113.229	β = 90
c = 138.615	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2019-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.8	50	96.9	0.164	0.054	1	13.2	8.2		15032			47.78

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	96.1		0.967	0.328	0.895	1.7	8

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	Rosetta modelling	2.8	29.25	11830	612	81.1	0.24217	0.24112	0.24	0.26295	0.26	RANDOM	61.372

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]
2.26			-3.97		1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.237
r_long_range_B_refined	18.218
r_long_range_B_other	18.218
r_dihedral_angle_3_deg	16.099
r_dihedral_angle_4_deg	14.948
r_scangle_other	12.484
r_mcangle_other	11.827
r_mcangle_it	11.818
r_scbond_it	9.052
r_scbond_other	9.049
r_mcbond_it	8.562
r_mcbond_other	8.537
r_dihedral_angle_1_deg	4.494
r_angle_refined_deg	1.44
r_angle_other_deg	0.805
r_chiral_restr	0.073
r_gen_planes_refined	0.042
r_gen_planes_other	0.036
r_bond_refined_d	0.008
r_bond_other_d	0.007
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	2761
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	177

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing