2VVD

Crystal structure of the receptor binding domain of the spike protein P1 from bacteriophage PM2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.57.4MG/ML PROTEIN (IN 150MM NACL AND 20MM TRIS PH 7.5), 20%(W/V) PEG3350, 200MM CACL2
Crystal Properties
Matthews coefficientSolvent content
1.9436.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.645α = 90
b = 49.055β = 90
c = 72.177γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-06-22MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97912,0.90499ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.2621.6900.0546.512.16935-314.65
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.3352.50.0827.77.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUTNONE2.2621.6652136989.80.1720.1690.228RANDOM16.3
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]
-0.590.230.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.875
r_dihedral_angle_4_deg17.924
r_dihedral_angle_3_deg11.205
r_dihedral_angle_1_deg6.21
r_scangle_it1.25
r_angle_refined_deg0.966
r_scbond_it0.887
r_angle_other_deg0.77
r_mcangle_it0.455
r_mcbond_it0.259
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.875
r_dihedral_angle_4_deg17.924
r_dihedral_angle_3_deg11.205
r_dihedral_angle_1_deg6.21
r_scangle_it1.25
r_angle_refined_deg0.966
r_scbond_it0.887
r_angle_other_deg0.77
r_mcangle_it0.455
r_mcbond_it0.259
r_symmetry_vdw_other0.19
r_nbd_other0.188
r_nbd_refined0.181
r_nbtor_refined0.175
r_symmetry_hbond_refined0.12
r_symmetry_vdw_refined0.119
r_xyhbond_nbd_refined0.117
r_nbtor_other0.078
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1284
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing