5M4V | pdb_00005m4v

X-ray structure of the mambaquaretin-1, a selective antagonist of the vasopressin type 2 receptor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B0C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	Protein: 7 mg/mL in 50mM sodium Acetate pH 5.5 Precipitant: 36% MPEG 2K, 0.45 M NaCl, 0.9 M KSCN, 0.1 M imidazole HCl, pH 7.5. Cryoprotectant: 5 % diethylene glycol, 5 % ethylene glycol, 5 % MPD, 5 % glycerol, 5 % 1,2-propanediol, 5 % DMSO, 18% MPEG-2K, 100 mM linear mixed buffer 1: sodium acetate, ADA, and bicine, 20% at pH 4 and 80% at pH 10.

Crystal Properties
Matthews coefficient	Solvent content
2.62	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.84	α = 90
b = 63.84	β = 90
c = 32.96	γ = 90

Symmetry
Space Group	P 4 21 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 PILATUS 6M	MIRRORS	2012-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976251	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	1.06	45.14	99.9	0.08	0.078	1	19.36	23.75		31490		-3	16

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.06	1.09	99.3		2.84	0.618	1.22	19.16

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	1B0C	1.06	45.14	29915	1575	99.9	0.13195	0.13067	0.13	0.15574	0.16	RANDOM	19.648

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]
0.08			0.08		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	32.975
r_dihedral_angle_2_deg	28.483
r_dihedral_angle_4_deg	18.121
r_dihedral_angle_3_deg	14.822
r_sphericity_bonded	12.152
r_dihedral_angle_1_deg	6.756
r_rigid_bond_restr	6.636
r_long_range_B_refined	6.383
r_long_range_B_other	5.299
r_scbond_it	3.377
r_scbond_other	3.358
r_scangle_other	3.317
r_angle_refined_deg	2.709
r_mcangle_it	2.057
r_mcangle_other	2.054
r_mcbond_it	1.849
r_mcbond_other	1.615
r_angle_other_deg	1.38
r_chiral_restr	0.134
r_bond_refined_d	0.029
r_gen_planes_refined	0.014
r_bond_other_d	0.013
r_gen_planes_other	0.005
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	448
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building