2I24

Crystal structure analysis of the nurse shark New Antigen Receptor PBLA8 variable domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	277	24% PEG 400, 0.1M Na/K phosphate, 0.15M NaCl, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.958	α = 90
b = 53.958	β = 90
c = 79.077	γ = 90

Symmetry
Space Group	P 43 21 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 210		2005-01-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.97623	ALS	8.2.1

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	1.35	44.7	98.7	0.056	16.7	3.8	26060	26060		-3	14

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)
	1.35	1.37	95.6		0.46	1.9	1.95	1226

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1SQ2, CHAIN N	1.35	44.7	24753	24753	1253	98.71	0.1741	0.17212	0.2143	RANDOM	17.858

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]
-0.37			-0.37		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.123
r_dihedral_angle_4_deg	16.629
r_dihedral_angle_3_deg	9.976
r_sphericity_free	9.864
r_dihedral_angle_1_deg	6.18
r_scangle_it	5.339
r_scbond_it	4.469
r_sphericity_bonded	4.061
r_mcangle_it	3.02
r_mcbond_it	2.569
r_rigid_bond_restr	2.132
r_angle_refined_deg	1.802
r_angle_other_deg	0.998
r_mcbond_other	0.797
r_symmetry_vdw_other	0.327
r_nbd_other	0.221
r_nbd_refined	0.199
r_nbtor_refined	0.177
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.129
r_nbtor_other	0.085
r_symmetry_vdw_refined	0.058
r_bond_refined_d	0.022
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	872
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
EPMR	phasing