3EHU | pdb_00003ehu

Crystal structure of the extracellular domain of human corticotropin releasing factor receptor type 1 (CRFR1) in complex with CRF

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.75	293	PEG MME 550, calcium chloride, tert-butanol, Bis-Tris, pH 6.75, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.203	α = 99.75
b = 63.48	β = 106.28
c = 85.875	γ = 101.67

Symmetry
Space Group	P 1

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				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	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	1.96	50	94.7	0.113	13.49	3.4		64919		-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)
1	1.96	2.03	75.2		0.337	2.32

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 entries 3C4M, 3EHS	1.96	39.5	61357	3254	94.93	0.212	0.209	0.21	0.256	0.25	RANDOM	30.115

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]
-0.42	0.9	0.38	1.73	-0.24	-0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.488
r_dihedral_angle_4_deg	18.572
r_dihedral_angle_3_deg	14.316
r_dihedral_angle_1_deg	5.426
r_scangle_it	2.649
r_scbond_it	1.713
r_angle_refined_deg	1.285
r_mcangle_it	1.029
r_mcbond_it	0.653
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.488
r_dihedral_angle_4_deg	18.572
r_dihedral_angle_3_deg	14.316
r_dihedral_angle_1_deg	5.426
r_scangle_it	2.649
r_scbond_it	1.713
r_angle_refined_deg	1.285
r_mcangle_it	1.029
r_mcbond_it	0.653
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.23
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.083
r_metal_ion_refined	0.068
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7044
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	90

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
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.