3H6N

Crystal Structure of the ubiquitin-like domain of plexin D1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	298	1.39M sodium citrate, 0.1M sodium cacodylate. The protein stock solution was adjusted to contain 15 mM TCEP, supplemented with 1:100 (w/w) chymotrypsin, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.777	α = 90
b = 27.051	β = 114.06
c = 52.653	γ = 90

Symmetry
Space Group	C 1 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		CCD	ADSC QUANTUM 315		2009-03-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97942	APS	19-ID

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	30	99.5	0.086	9.6	4.4		7245

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)
	2	2.03	99.7		0.499		3.6	381

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.004	30	7229	337	98.865	0.244	0.243	0.276	RANDOM	31.154

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]
-1.706		-0.265	1.444		0.046

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.446
r_dihedral_angle_4_deg	20.348
r_dihedral_angle_3_deg	14.389
r_dihedral_angle_1_deg	6.012
r_scangle_it	1.814
r_mcangle_it	1.651
r_scbond_it	1.305
r_angle_refined_deg	1.095
r_mcbond_it	0.983
r_angle_other_deg	0.748
r_mcbond_other	0.217
r_chiral_restr	0.062
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	775
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	3

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction