2QQL

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		297	10% PEG 1000, 10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.406	α = 90
b = 121.406	β = 90
c = 202.717	γ = 120

Symmetry
Space Group	P 32 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	3.1	50	99.6	0.061	18.3	3.8		31929			102

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	3.1	3.21	98.9		0.515	2.6	3.6	3101

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	PDB entry 2QQK	3.1	30	30265	1610	99.69	0.19	0.188	0.232	RANDOM	97.086

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]
-2.13	-1.07		-2.13		3.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.682
r_dihedral_angle_3_deg	18.277
r_dihedral_angle_4_deg	17.306
r_dihedral_angle_1_deg	7.316
r_mcangle_it	3.85
r_scangle_it	3.36
r_mcbond_it	2.754
r_scbond_it	2.212
r_angle_refined_deg	1.309
r_angle_other_deg	0.828
r_mcbond_other	0.452
r_symmetry_vdw_other	0.206
r_nbd_refined	0.205
r_symmetry_hbond_refined	0.204
r_nbd_other	0.191
r_nbtor_refined	0.188
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.157
r_nbtor_other	0.087
r_chiral_restr	0.073
r_bond_refined_d	0.01
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	7740
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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