2X3M

Crystal Structure of Hypothetical Protein ORF239 from Pyrobaculum Spherical Virus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG 3350, 0.2M POTASSIUM ACETATE CRYOPROTECTION WITH 20% PEG 400
Crystal Properties
Matthews coefficientSolvent content
2.0139

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.898α = 90
b = 53.715β = 90
c = 95.193γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRRORS2007-03-21MSINGLE 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
11.451.5970.0428.34.439560
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)
11.451.5730.461.82.1

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 DIFFRACTIONSADTHROUGHOUTNONE1.4519.5636291192496.70.1780.1770.195RANDOM16.73
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]
0.08-0.04-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.432
r_dihedral_angle_4_deg14.704
r_dihedral_angle_3_deg11.679
r_sphericity_free5.254
r_dihedral_angle_1_deg4.053
r_scangle_it3.59
r_rigid_bond_restr2.568
r_sphericity_bonded2.52
r_scbond_it2.411
r_mcangle_it1.546
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.432
r_dihedral_angle_4_deg14.704
r_dihedral_angle_3_deg11.679
r_sphericity_free5.254
r_dihedral_angle_1_deg4.053
r_scangle_it3.59
r_rigid_bond_restr2.568
r_sphericity_bonded2.52
r_scbond_it2.411
r_mcangle_it1.546
r_mcbond_it0.918
r_angle_refined_deg0.916
r_angle_other_deg0.792
r_mcbond_other0.344
r_chiral_restr0.059
r_bond_refined_d0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1347
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling