2QQN

Neuropilin-1 b1 Domain in Complex with a VEGF-Blocking Fab

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KEX	1KEX (b1 domain), 2FJH (Fab)
experimental model	PDB	2FJH	1KEX (b1 domain), 2FJH (Fab)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	25% PEG 1500, 4% tert-butanol, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 214.115	α = 90
b = 214.115	β = 90
c = 45.465	γ = 120

Symmetry
Space Group	H 3

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	MARMOSAIC 325 mm CCD		2006-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979	SSRL	BL11-1

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	2.2	50	99	0.096	14.3	4.4		39195			41.1

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	2.2	2.28	98		0.485	2.2	3.6	3893

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	1KEX (b1 domain), 2FJH (Fab)	2.2	20	37085	1976	99.06	0.162	0.159	0.207	RANDOM	33.243

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]
0.16	0.08		0.16		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.918
r_dihedral_angle_4_deg	21.285
r_dihedral_angle_3_deg	13.805
r_dihedral_angle_1_deg	6.906
r_scangle_it	5.051
r_mcangle_it	4.335
r_scbond_it	3.61
r_mcbond_it	3.523
r_angle_refined_deg	1.427
r_angle_other_deg	0.886
r_mcbond_other	0.713
r_symmetry_vdw_other	0.197
r_nbd_other	0.196
r_nbd_refined	0.178
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.16
r_symmetry_vdw_refined	0.159
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.09
r_nbtor_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4540
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	12

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