3BUK

Crystal Structure of the Neurotrophin-3 and p75NTR Symmetrical Complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	5	290	0.9M Lithium Sulfate, 0.05M Na Citrate, 0.7M Ammonium Sulfate, pH 5.0, EVAPORATION, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.8	α = 90
b = 125.8	β = 90
c = 133.1	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	113	CCD	MAR CCD 165 mm		2007-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.0030	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.6	50	96.2	0.06		4		23326			42

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.66	97.3		0.381		3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1NT3	2.6	50	22069	22069	1190	96.18	0.22749	0.22749	0.22422	0.28771	RANDOM	45.243

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]
0.98	0.49		0.98		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.964
r_dihedral_angle_4_deg	22.814
r_dihedral_angle_3_deg	22.348
r_dihedral_angle_1_deg	8.952
r_scangle_it	2.942
r_mcangle_it	2.617
r_scbond_it	2.053
r_angle_refined_deg	1.725
r_mcbond_it	1.473
r_nbtor_refined	0.314
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.242
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.128
r_symmetry_hbond_refined	0.076
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4080
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing