7P5U

Neuropilin-b1 in a complex with a VEGFB-derived peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	10 to 30% PEG 3350 + 0.2 M ammonium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.496	α = 90
b = 74.35	β = 90
c = 91.426	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2015-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.51	57.684	96.7	0.067	14	7.9		50849

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	1.6	1.67			0.73

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1KEX	1.6	57.68	44108	2189	99.36	0.189	0.1882	0.2139	19.547

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]
0.034			-0.029		-0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.356
r_dihedral_angle_4_deg	21.08
r_dihedral_angle_3_deg	14.118
r_dihedral_angle_1_deg	7.903
r_lrange_it	5.58
r_lrange_other	5.579
r_scangle_it	4.219
r_scangle_other	4.219
r_mcangle_it	2.799
r_mcangle_other	2.799
r_scbond_it	2.778
r_scbond_other	2.778
r_angle_refined_deg	1.944
r_mcbond_it	1.862
r_mcbond_other	1.861
r_angle_other_deg	1.51
r_nbd_other	0.277
r_symmetry_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.19
r_nbd_refined	0.183
r_nbtor_refined	0.176
r_xyhbond_nbd_other	0.174
r_xyhbond_nbd_refined	0.141
r_ncsr_local_group_1	0.119
r_chiral_restr	0.1
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2536
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing