4CYY | pdb_00004cyy

The structure of vanin-1: defining the link between metabolic disease, oxidative stress and inflammation

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CYF	PDB ENTRY 4CYF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6		THE PROTEIN WAS AT 15 MG/ML. THE RESERVOIR CONDITIONS WERE 25% (W/V) PEG 1500 PLUS 10% (V/V) SUCCINATE-PHOSPHATE-GLYCINE BUFFER AT PH 6.0. THE PLATES WERE SET UP AT 8 C AND THE DROPS WERE 150 NL PLUS 150 NL IN SITTING DROP PLATES.

Crystal Properties
Matthews coefficient	Solvent content
3.91	68.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.904	α = 90
b = 101.904	β = 90
c = 133.652	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC CCD		2013-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2		Australian Synchrotron	MX2

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	2.89	47.6	99.7	0.21	14.5	16.3		18526

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	2.89	3.04	97.9		1.12	2.7	16.1

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 4CYF	2.89	88.25	17545	947	99.62	0.17646	0.17425	0.18	0.21883	0.22	RANDOM	61.539

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]
2.84	1.42		2.84		-9.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.198
r_dihedral_angle_4_deg	18.372
r_dihedral_angle_3_deg	15.288
r_dihedral_angle_1_deg	7.031
r_mcangle_it	4.309
r_scbond_it	3.816
r_mcbond_it	2.677
r_mcbond_other	2.675
r_angle_refined_deg	1.322
r_angle_other_deg	0.71
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3615
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing