2QQI

Crystal Structure of the b1b2 Domains from Human Neuropilin-1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	20% PEG 3350, 0.2 M Sodium Fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.92	α = 90
b = 66.979	β = 90
c = 74.679	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	CCD	ADSC QUANTUM 315		2003-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

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	1.8	50	97.6	0.05	26.9	4.6		30653			26.2

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	1.8	1.86	99.3		0.515	3.2	4.6	3047

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 1KEX	1.8	20	29018	1526	97.67	0.161	0.159	0.201	RANDOM	26.584

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]
-1.58			0.32		1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.853
r_dihedral_angle_4_deg	15.348
r_dihedral_angle_3_deg	12.126
r_dihedral_angle_1_deg	6.553
r_scangle_it	4.711
r_mcangle_it	3.904
r_scbond_it	3.519
r_mcbond_it	3.397
r_angle_refined_deg	1.5
r_angle_other_deg	0.894
r_mcbond_other	0.708
r_symmetry_vdw_other	0.256
r_symmetry_vdw_refined	0.233
r_nbd_other	0.203
r_nbd_refined	0.188
r_nbtor_refined	0.183
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.096
r_nbtor_other	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2514
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	6

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