2QQM | pdb_00002qqm

Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QQI	2QQI (b1b2 domains), 2QQK (a2 domain)
experimental model	PDB	2QQK	2QQI (b1b2 domains), 2QQK (a2 domain)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	297	0.1 M MES, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.177	α = 90
b = 68.178	β = 102.1
c = 66.613	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	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	50	97.5	0.086	13.8	3.5		30901			30.9

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	2.07	88.7		0.322	3.2	3	2794

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QQI (b1b2 domains), 2QQK (a2 domain)	2	20	29213	1558	97.55	0.186	0.183	0.19	0.243	0.25	RANDOM	36.27

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]
-2.38		2.16	-1.22		4.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.335
r_dihedral_angle_4_deg	18.699
r_dihedral_angle_3_deg	13.546
r_dihedral_angle_1_deg	6.631
r_mcangle_it	4.666
r_scangle_it	4.572
r_mcbond_it	3.511
r_scbond_it	3.314
r_angle_refined_deg	1.455
r_angle_other_deg	0.843
r_mcbond_other	0.843
r_symmetry_vdw_refined	0.234
r_symmetry_vdw_other	0.213
r_nbd_other	0.195
r_nbd_refined	0.185
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.126
r_metal_ion_refined	0.105
r_nbtor_other	0.096
r_chiral_restr	0.083
r_bond_refined_d	0.012
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	3456
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	101

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