9PLP | pdb_00009plp

Crystal structure of netrin-1 in complex with anti-netrin-1 Fab (NP137 Fab)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LRF
experimental model	PDB	9OHH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	18% PEG8000, 100 mM HEPES pH 7.5, 200 mM Ca Acetate

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.984	α = 90
b = 263.049	β = 92.512
c = 68.765	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS3 6M		2021-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	4.99	49.39	97.08	0.99	5.4	3.3		9577

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.99	5.41			0.48

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	4.99	49.39	9567	966	90.967	0.29	0.2861	0.3026	0.3211	0.3068	RANDOM	48.504

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]
-59.209		-2.1	-71.782		130.991

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.506
r_dihedral_angle_6_deg	13.515
r_dihedral_angle_1_deg	6.419
r_angle_refined_deg	1.04
r_angle_other_deg	0.38
r_metal_ion_refined	0.254
r_symmetry_nbd_other	0.203
r_xyhbond_nbd_refined	0.186
r_nbd_refined	0.185
r_nbtor_refined	0.171
r_nbd_other	0.147
r_ncsr_local_group_1	0.102
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_nbd_refined	0.093
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_3	0.074
r_ncsr_local_group_2	0.071
r_chiral_restr	0.05
r_ext_dist_refined_b	0.03
r_bond_refined_d	0.008
r_symmetry_xyhbond_nbd_refined	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10403
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing