2R9U

Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2O6R	PDB ENTRY 2O6R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	2.0-2.4 M NaH2PO4/K2HPO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.109	α = 90
b = 61.057	β = 107.35
c = 98.081	γ = 90

Symmetry
Space Group	P 1 21 1

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	MarUSA MarMosaic -325	Flat Mirror	2007-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.98	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	2.1	50	91.3	0.115	9	3.1		43844

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	2.1	2.18	81.3		0.293	3	2.8	3847

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2O6R	2.1	50	41594	2232	91.06	0.22	0.217	0.264	RANDOM	20.107

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]
3.91		-0.36	-1.39		-2.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.543
r_dihedral_angle_4_deg	23.63
r_dihedral_angle_3_deg	13.423
r_dihedral_angle_1_deg	6.324
r_scangle_it	5.945
r_scbond_it	4.526
r_mcangle_it	2.272
r_angle_refined_deg	1.654
r_mcbond_it	1.54
r_angle_other_deg	1.068
r_mcbond_other	0.313
r_symmetry_vdw_other	0.309
r_symmetry_vdw_refined	0.269
r_nbd_refined	0.21
r_nbd_other	0.21
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.181
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.096
r_nbtor_other	0.09
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5456
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
HKL-2000	data reduction
HKL-2000	data scaling
CaspR	phasing