1SQ2

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LKSPDB ENTRIES 1LKS AND 1QLE (residues 1-85)
experimental modelPDB 1QLEPDB ENTRIES 1LKS AND 1QLE (residues 1-85)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729515% PEG 10,000, 0.1M imidazole HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal Properties
Matthews coefficientSolvent content
2.2645.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.02α = 90
b = 109.84β = 90
c = 29.28γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-01-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1159ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.453593.10.05437.94.64048240482-317
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4852.60.3942

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 1LKS AND 1QLE (residues 1-85)1.45354041040410202593.160.197440.196010.22534RANDOM16.334
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]
-0.1-0.310.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.18
r_dihedral_angle_4_deg17.499
r_dihedral_angle_3_deg12.588
r_dihedral_angle_1_deg6.097
r_scangle_it3.835
r_scbond_it2.875
r_mcangle_it1.957
r_angle_refined_deg1.724
r_mcbond_it1.615
r_angle_other_deg0.938
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.18
r_dihedral_angle_4_deg17.499
r_dihedral_angle_3_deg12.588
r_dihedral_angle_1_deg6.097
r_scangle_it3.835
r_scbond_it2.875
r_mcangle_it1.957
r_angle_refined_deg1.724
r_mcbond_it1.615
r_angle_other_deg0.938
r_mcbond_other0.356
r_symmetry_vdw_other0.255
r_nbd_refined0.229
r_nbd_other0.2
r_symmetry_hbond_refined0.183
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.159
r_chiral_restr0.123
r_nbtor_other0.084
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1835
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing