2X5R

Crystal Structure of the hypothetical protein ORF126 from Pyrobaculum spherical virus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1811% PEGMME 550, 0.04M ZN SULPHATE AND 0.1M TRIS HCL PH8. CRYSTAL WAS CRYOPROTECTED IN 12% PEGMME 550, 0.01M ZN SULPHATE AND 0.1M TRIS HCL PH8 AND 25% PEG400 SOLUTION
Crystal Properties
Matthews coefficientSolvent content
2.345.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.041α = 90
b = 39.041β = 90
c = 143.733γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2007-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.92097.30.0711.23.88611
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)
11.92950.4233.7

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 DIFFRACTIONSADTHROUGHOUTNONE224.63861140997.80.207140.20540.24553RANDOM17.003
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]
-0.29-0.15-0.290.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.141
r_dihedral_angle_3_deg15.515
r_dihedral_angle_4_deg12.542
r_dihedral_angle_1_deg5.497
r_scangle_it1.72
r_angle_refined_deg1.129
r_scbond_it1
r_mcangle_it0.85
r_angle_other_deg0.789
r_mcbond_it0.464
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.141
r_dihedral_angle_3_deg15.515
r_dihedral_angle_4_deg12.542
r_dihedral_angle_1_deg5.497
r_scangle_it1.72
r_angle_refined_deg1.129
r_scbond_it1
r_mcangle_it0.85
r_angle_other_deg0.789
r_mcbond_it0.464
r_mcbond_other0.08
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms959
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing