2WKD

Crystal structure of a double Ile-to-Met mutant of protein ORF34 from lactococcus phage p2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2PROTEIN AT 7 MG/ML IN 10 MM TRIS, 300 MM NACL, 1 MM TCEP, PH 8.0 WAS CRYSTALLIZED BY SITTING-DROP VAPOUR DIFFUSION AGAINST 0.1 M HEPES PH 7.2, 60% MME-PEG550
Crystal Properties
Matthews coefficientSolvent content
4.2270.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.74α = 90
b = 75.74β = 90
c = 88.04γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 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
12.188.0499.80.0525.7910.189205-340
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)
12.12.121000.443.7710.54

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 DIFFRACTIONSADTHROUGHOUTNONE2.144.02918291899.7830.240.23860.2562RANDOM55.7
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]
3.1521.5763.152-4.728
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.812
r_dihedral_angle_4_deg24.773
r_dihedral_angle_3_deg16.688
r_scangle_it6.543
r_dihedral_angle_1_deg5.932
r_scbond_it4.315
r_mcangle_it2.53
r_mcbond_it1.626
r_angle_refined_deg1.186
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.812
r_dihedral_angle_4_deg24.773
r_dihedral_angle_3_deg16.688
r_scangle_it6.543
r_dihedral_angle_1_deg5.932
r_scbond_it4.315
r_mcangle_it2.53
r_mcbond_it1.626
r_angle_refined_deg1.186
r_nbtor_refined0.305
r_nbd_refined0.198
r_symmetry_hbond_refined0.141
r_symmetry_vdw_refined0.131
r_xyhbond_nbd_refined0.111
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms610
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
TRUNCATEdata scaling
SHELXphasing