1SQ2

Crystal Structure Analysis of the Nurse Shark New Antigen Receptor (NAR) Variable Domain in Complex With Lysozyme

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LKS	PDB ENTRIES 1LKS AND 1QLE (residues 1-85)
experimental model	PDB	1QLE	PDB ENTRIES 1LKS AND 1QLE (residues 1-85)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	15% PEG 10,000, 0.1M imidazole HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.02	α = 90
b = 109.84	β = 90
c = 29.28	γ = 90

Symmetry
Space Group	P 21 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		2004-01-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1159	ALS	8.3.1

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	1.45	35	93.1	0.054	37.9	4.6	40482	40482		-3	17

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	1.45	1.48	52.6		0.394	2

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 ENTRIES 1LKS AND 1QLE (residues 1-85)	1.45	35	40410	40410	2025	93.16	0.19744	0.19601	0.22534	RANDOM	16.334

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]
-0.1			-0.31		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.18
r_dihedral_angle_4_deg	17.499
r_dihedral_angle_3_deg	12.588
r_dihedral_angle_1_deg	6.097
r_scangle_it	3.835
r_scbond_it	2.875
r_mcangle_it	1.957
r_angle_refined_deg	1.724
r_mcbond_it	1.615
r_angle_other_deg	0.938
r_mcbond_other	0.356
r_symmetry_vdw_other	0.255
r_nbd_refined	0.229
r_nbd_other	0.2
r_symmetry_hbond_refined	0.183
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.123
r_nbtor_other	0.084
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1835
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing