2QQK

Neuropilin-2 a1a2b1b2 Domains in Complex with a Semaphorin-Blocking Fab

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QQJ	2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain)
experimental model	PDB	2FJH	2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain)
experimental model	PDB	1NT0	2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	297	0.1 M Hepes, 22% polyacrylic acid 5100, 0.02 M MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.277	α = 90
b = 105.873	β = 98.83
c = 92.4	γ = 90

Symmetry
Space Group	C 1 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	ADSC QUANTUM 315		2006-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.75	50	99.6	0.104	10.9	4.2		36321			75.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.85	100		0.527	3.3	4.2	3599

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QQJ (b1b2 domains), 2FJH (antibody), 1NT0 (a2 domain)	2.75	30	34487	1830	98.99	0.189	0.186	0.243	RANDOM	74.912

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]
2.09		-2.82	4.17		-7.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.051
r_dihedral_angle_3_deg	16.882
r_dihedral_angle_4_deg	14.513
r_dihedral_angle_1_deg	6.807
r_mcangle_it	4.297
r_scangle_it	4.212
r_mcbond_it	3.256
r_scbond_it	2.917
r_angle_refined_deg	1.258
r_angle_other_deg	0.826
r_mcbond_other	0.504
r_symmetry_vdw_other	0.217
r_nbd_refined	0.193
r_nbd_other	0.188
r_nbtor_refined	0.185
r_symmetry_hbond_refined	0.175
r_symmetry_vdw_refined	0.156
r_xyhbond_nbd_refined	0.12
r_nbtor_other	0.084
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7593
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	28

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction