2QQO

Crystal Structure of the a2b1b2 Domains from Human Neuropilin-2

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), 2QQK (a2 domain)
experimental model	PDB	2QQK	2QQJ (b1b2 domains), 2QQK (a2 domain)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	297	0.1 M Hepes, 10% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.093	α = 90
b = 192.909	β = 90.08
c = 66.169	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	100	CCD	ADSC QUANTUM 210		2007-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.00	ALS	5.0.1

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	2.3	50	94.5	0.056	14	4.2		52659

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	2.3	2.38	85.6		0.344	3.7	4.1	4766

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), 2QQK (a2 domain)	2.3	20	49667	2679	94.47	0.188	0.185	0.239	RANDOM	31.764

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]
0.27		0.02	0.08		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.285
r_dihedral_angle_4_deg	19.607
r_dihedral_angle_3_deg	14.393
r_dihedral_angle_1_deg	7.149
r_scangle_it	4.605
r_mcangle_it	4.345
r_scbond_it	3.348
r_mcbond_it	3.108
r_angle_refined_deg	1.44
r_angle_other_deg	0.897
r_mcbond_other	0.861
r_symmetry_vdw_other	0.204
r_nbd_other	0.195
r_nbd_refined	0.179
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.153
r_symmetry_vdw_refined	0.143
r_symmetry_hbond_refined	0.14
r_metal_ion_refined	0.109
r_chiral_restr	0.087
r_nbtor_other	0.083
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	6813
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	34

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