2V5I

Structure of the receptor-binding protein of bacteriophage Det7: a podoviral tailspike in a myovirus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TSPPDB ENTRY 1TSP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.510 TO 30 % (W/V) PEG4000, 0.1 M SODIUM CITRATE PH 4.5, 0 TO 15 % (V/V) GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.433α = 90
b = 100.433β = 90
c = 330.042γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHSILICON TOROIDAL MIRROR2004-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.61594.60.0813.15.28018914.48
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)
11.61.6985.90.253.84.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1TSP1.61578590159894.60.1420.1410.17RANDOM13.12
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]
0.950.480.95-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.123
r_dihedral_angle_4_deg13.375
r_dihedral_angle_3_deg12.264
r_dihedral_angle_1_deg6.587
r_scangle_it5.61
r_scbond_it3.666
r_mcangle_it2.434
r_angle_refined_deg1.655
r_mcbond_it1.418
r_angle_other_deg0.888
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.123
r_dihedral_angle_4_deg13.375
r_dihedral_angle_3_deg12.264
r_dihedral_angle_1_deg6.587
r_scangle_it5.61
r_scbond_it3.666
r_mcangle_it2.434
r_angle_refined_deg1.655
r_mcbond_it1.418
r_angle_other_deg0.888
r_symmetry_vdw_other0.215
r_nbd_refined0.196
r_nbd_other0.183
r_nbtor_refined0.169
r_symmetry_vdw_refined0.151
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.132
r_chiral_restr0.121
r_nbtor_other0.08
r_bond_refined_d0.018
r_gen_planes_refined0.009
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 Atoms4143
Nucleic Acid Atoms
Solvent Atoms831
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing