4CYG | pdb_00004cyg

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	6.5	281	CRYSTALLIZATION CONDITIONS: PROTEIN AT 12 MG/ML IN 50 MM BIS-TRIS PH 6.5 WITH 50 MM NACL. RESERVOIR CONDITIONS WERE 21% PEG 1500 WITH 10% (V/V) MALATE-MES-TRIS BUFFER AT PH 6.3. DROPS WERE 200 NL PLUS 200 NL IN SITTING DROP PLATES AT 8C.

Crystal Properties
Matthews coefficient	Solvent content
3.88	68.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.093	α = 90
b = 120.093	β = 90
c = 221.9	γ = 90

Symmetry
Space Group	P 43 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	CCD	ADSC CCD		2013-11-29	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	2.3	48.3	99.6	0.15	15.6	14.9		72390

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	2.3	2.42	99.3		1.24	2.6	15.2

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	2.3	105.62	68703	3638	99.42	0.18765	0.18624	0.19	0.21444	0.22	RANDOM	36.863

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]
0.24			0.24		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.508
r_dihedral_angle_4_deg	17.562
r_dihedral_angle_3_deg	12.708
r_dihedral_angle_1_deg	6.551
r_mcangle_it	3.134
r_scbond_it	2.577
r_mcbond_it	1.962
r_mcbond_other	1.959
r_angle_refined_deg	1.24
r_angle_other_deg	0.82
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	7267
Nucleic Acid Atoms
Solvent Atoms	307
Heterogen Atoms	168

Software

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