3AL8 | pdb_00003al8

Plexin A2 / Semaphorin 6A complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	18-25% (wt./vol.) PEG 1000, 0.2-0.3M MgCl2, 0.1M Na-cacodylate pH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.99	75.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 240.87	α = 90
b = 240.87	β = 90
c = 146.745	γ = 120

Symmetry
Space Group	P 61 2 2

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 270		2009-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0000	Photon Factory	BL-17A

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	3.6	49.15	99.5	0.097	17.1	6.5		29317		-3	59.723

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)
	3.6	3.79	99.8		0.417	4	6.6	4222

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3.6	49.15	27830	1483	99.24	0.23316	0.23039	0.222	0.28733	0.2761	RANDOM	99.662

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]
1.62	0.81		1.62		-2.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.049
r_dihedral_angle_4_deg	18.948
r_dihedral_angle_3_deg	18.203
r_dihedral_angle_1_deg	6.012
r_scangle_it	1.13
r_angle_refined_deg	1.098
r_mcangle_it	0.827
r_scbond_it	0.612
r_mcbond_it	0.45
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8148
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	181

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling