9D77 | pdb_00009d77

Crystal form of Netrin-1 mimics nanotubes

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LRF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	40% v/v 2-methyl-2,4-pentanediol; 5% w/v polyethylene glycol 8000; 100 mM 2-(N-morpholino)ethanesulfonic acid; pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
4.53	72.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 189.26	α = 90
b = 189.26	β = 90
c = 45.88	γ = 120

Symmetry
Space Group	P 6

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	Rigaku Osmic Confocal Max-Flux multilayer mirror	2017-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.4	35.77	68.9	0.412	0.435	0.14	0.994	4.9	9.6		9185			83.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	4.2	33.53		1.473	1.553	0.488	0.583	1.9	9.8

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 (All)	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	3.4	35.77	9185	743	68.74	0.3	0.2967	0.2904	0.3348	0.3252	Random selection	88.104

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]
-4.198	-2.099		-4.198		13.618

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.949
r_dihedral_angle_6_deg	14.042
r_dihedral_angle_1_deg	10.352
r_dihedral_angle_other_1_deg	8.932
r_dihedral_angle_2_deg	7.406
r_lrange_it	2.853
r_lrange_other	2.853
r_angle_refined_deg	1.847
r_scangle_it	1.532
r_scangle_other	1.532
r_scbond_it	0.864
r_scbond_other	0.864
r_mcangle_it	0.61
r_mcangle_other	0.61
r_angle_other_deg	0.6
r_dihedral_angle_other_3_deg	0.478
r_mcbond_it	0.338
r_mcbond_other	0.338
r_xyhbond_nbd_refined	0.281
r_symmetry_nbd_other	0.195
r_symmetry_xyhbond_nbd_refined	0.182
r_nbd_refined	0.181
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.162
r_nbd_other	0.162
r_symmetry_nbtor_other	0.107
r_symmetry_nbd_refined	0.105
r_chiral_restr	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3272
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	225

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building