6DK5 | pdb_00006dk5

The X-ray crystal structure of human endothelin-1, a polypeptide hormone regulator of blood pressure

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	310	4 uL 15 mg/mL aqueous endothelin + 6 uL reservoir solution (20-25% MPD, 0.2 M MES, pH 6.5) + 2 uL 0.2 M MES, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.71	29.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.328	α = 90
b = 27.328	β = 90
c = 79.538	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	AREA DETECTOR	SDMS		1997-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.85	80	99.6	0.257	0.257	0.283	0.086	0.947	4.6	7.7		2534

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 5GLH	1.85	23.67	2534	143	92.92	0.2079	0.20387	0.22	0.28373	0.29	RANDOM	32.583

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]
0.01	0.01		0.01		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.176
r_dihedral_angle_3_deg	20.16
r_dihedral_angle_1_deg	8.03
r_long_range_B_refined	7.759
r_long_range_B_other	7.752
r_mcangle_it	4.635
r_mcangle_other	4.629
r_scangle_other	3.994
r_mcbond_it	3.171
r_mcbond_other	3.144
r_scbond_it	2.696
r_scbond_other	2.69
r_angle_refined_deg	1.632
r_angle_other_deg	0.883
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	334
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms

Software

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