2VFM

Low Temperature Structure of P22 Tailspike Protein Fragment (109-666)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110DROP: 2 MICROLITER 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0, PLUS 3.3 MICROLITER 10 MG/ML PROTEIN SOLUTION IN 10 MM HEPES, PH 7.0; RESERVOIR: 750 MICOLITER 1.0 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0
Crystal Properties
Matthews coefficientSolvent content
2.448.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.9α = 90
b = 119.9β = 90
c = 119.9γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2007-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.595097.10.0437.910.67482818.1
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)
11.591.786.80.157.23.1

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 2VFQ1.539.9777129406087.90.1360.1350.164RANDOM10.27
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.898
r_dihedral_angle_4_deg13.333
r_dihedral_angle_3_deg11.915
r_dihedral_angle_1_deg6.857
r_scangle_it4.355
r_scbond_it3.244
r_mcangle_it2.059
r_mcbond_it1.565
r_angle_refined_deg1.33
r_angle_other_deg0.901
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.898
r_dihedral_angle_4_deg13.333
r_dihedral_angle_3_deg11.915
r_dihedral_angle_1_deg6.857
r_scangle_it4.355
r_scbond_it3.244
r_mcangle_it2.059
r_mcbond_it1.565
r_angle_refined_deg1.33
r_angle_other_deg0.901
r_symmetry_vdw_other0.239
r_nbd_other0.2
r_nbd_refined0.192
r_nbtor_refined0.17
r_symmetry_vdw_refined0.157
r_symmetry_hbond_refined0.148
r_xyhbond_nbd_refined0.136
r_chiral_restr0.081
r_nbtor_other0.081
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms4207
Nucleic Acid Atoms
Solvent Atoms825
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing