4OVE | pdb_00004ove

X-ray Crystal Structure of Mouse Netrin-1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	293	0.1 M HEPES, 2.7-2.8 M NaCl, 0.02-0.2 M glycine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.8	74.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.754	α = 90
b = 69.754	β = 90
c = 334.802	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	RAYONIX MX-300	vertical collimating mirror, toroidal focusing mirror	2011-10-14	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RAYONIX MX-225	dynamically bendable mirror	2005-10-12	M	SIRAS

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.25440	CLSI	08B1-1
2	SYNCHROTRON	SLS BEAMLINE X06SA	1.25470, 1.25520, 1.24210	SLS	X06SA

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	2.5	50	80.9	0.129	8.8	10.5	27279	27279			60.1

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	2.64	50	24458	1308	89.45	0.233	0.23	0.2371	0.288	0.2378	RANDOM	64.552

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]
-0.84	-0.42		-0.84		2.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.259
r_dihedral_angle_3_deg	18.164
r_dihedral_angle_4_deg	15.243
r_dihedral_angle_1_deg	13.261
r_mcangle_it	5.951
r_scbond_it	3.878
r_mcbond_other	3.622
r_mcbond_it	3.621
r_angle_refined_deg	1.806
r_angle_other_deg	0.857
r_chiral_restr	0.086
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.002
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	3309
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	105

Software

Software
Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling