9HYT | pdb_00009hyt

Crystal structure of the GFRaL receptor in complex with an inhibitory cyclic peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VZ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.3 M (NH4)2SO4, 0.1 M Na-citrate, 0.9 M LiSO4 100nL GFRaL-peptide mixture mixed with 80nL well solution and 20nL seed stock.

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.541	α = 90
b = 148.183	β = 90
c = 198.053	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	PIXEL	DECTRIS EIGER2 XE 16M		2019-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.980	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.9	99	92.5	0.999	11.2	3.5		38664

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.19			0.669

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	99	38663	1952	55.712	0.196	0.1938	0.2013	0.2445	0.247	5	33.964

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]
-0.109			-0.221		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.413
r_dihedral_angle_6_deg	14.616
r_dihedral_angle_2_deg	12.302
r_lrange_it	8.731
r_lrange_other	8.709
r_dihedral_angle_1_deg	6.563
r_scangle_it	6.48
r_scangle_other	6.424
r_mcangle_it	5.047
r_mcangle_other	5.046
r_scbond_it	4.218
r_scbond_other	4.158
r_mcbond_it	3.344
r_mcbond_other	3.339
r_angle_refined_deg	1.649
r_angle_other_deg	1.06
r_xyhbond_nbd_refined	0.423
r_symmetry_xyhbond_nbd_refined	0.245
r_nbd_other	0.24
r_nbd_refined	0.224
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.183
r_symmetry_nbd_refined	0.174
r_ncsr_local_group_1	0.084
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_2	0.082
r_ncsr_local_group_3	0.077
r_chiral_restr	0.075
r_bond_other_d	0.045
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4996
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing