2I25

Crystal structure analysis of the nurse shark New antigen Receptor PBLA8 variable domain in complex with lysozyme

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	38% PEG 400, 0.1M Tris, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.979	α = 90
b = 82.719	β = 90
c = 107.363	γ = 90

Symmetry
Space Group	P 21 21 21

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		2005-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.95369	SSRL	BL9-2

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	1.8	33.71	98.2	0.064	19.7	4.2	60320	60320		-3	28.3

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	1.8	1.85	100		0.535	1.7	4.1	4524

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	33.71	57232	57232	3041	100	0.18664	0.18532	0.21083	RANDOM	31.297

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]
0.63			-0.69		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.627
r_dihedral_angle_4_deg	15.69
r_dihedral_angle_3_deg	12.79
r_dihedral_angle_1_deg	6.379
r_scangle_it	3.922
r_scbond_it	2.808
r_angle_refined_deg	1.762
r_mcangle_it	1.687
r_mcbond_it	1.398
r_angle_other_deg	1.006
r_mcbond_other	0.364
r_symmetry_vdw_other	0.244
r_nbd_other	0.216
r_nbd_refined	0.215
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.11
r_nbtor_other	0.089
r_symmetry_vdw_refined	0.074
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3784
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms

Software

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