3L2J

Dimeric structure of the ligand-free extracellular domain of the human parathyroid hormone receptor (PTH1R)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C4M	pdb entry 3C4M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	ammonium sulfate, HEPES, sodium acetate, PEG400, cadaverine dihydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.702	α = 90
b = 182.326	β = 90
c = 97.166	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9785	APS	21-ID-F

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	3.24	50	99.8	0.11	12.59	4		19648		-3

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)
	3.24	3.36	98.5		0.493	1.94	3.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3C4M	3.24	50	19648	1016	99.82	0.227	0.225	0.258	RANDOM	79.286

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]
1.1			-2.07		0.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.37
r_dihedral_angle_4_deg	22.628
r_dihedral_angle_3_deg	17.635
r_dihedral_angle_1_deg	5.218
r_angle_refined_deg	1.078
r_scangle_it	0.858
r_scbond_it	0.52
r_nbtor_refined	0.303
r_mcangle_it	0.284
r_symmetry_hbond_refined	0.276

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.37
r_dihedral_angle_4_deg	22.628
r_dihedral_angle_3_deg	17.635
r_dihedral_angle_1_deg	5.218
r_angle_refined_deg	1.078
r_scangle_it	0.858
r_scbond_it	0.52
r_nbtor_refined	0.303
r_mcangle_it	0.284
r_symmetry_hbond_refined	0.276
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.197
r_mcbond_it	0.177
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7652
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.