1VK1

Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.52912.0M NaCl, 0.1M TRIS, pH 8.5, modified microbatch, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2946.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.148α = 90
b = 40.099β = 122.29
c = 65.671γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2003-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.25080.50.0434.32.4-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2421.50.144.11.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSINGLE WAVELENGTH ANOMALOUS SCATTERINGTHROUGHOUT1.255.963181337483.40.1660.1650.175RANDOM14.7
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]
-0.38-0.261.12-1.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.568
r_dihedral_angle_4_deg13.897
r_dihedral_angle_3_deg10.971
r_sphericity_free6.374
r_dihedral_angle_1_deg5.951
r_scangle_it3.701
r_sphericity_bonded3.239
r_mcangle_it2.792
r_scbond_it2.514
r_mcbond_it1.991
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.568
r_dihedral_angle_4_deg13.897
r_dihedral_angle_3_deg10.971
r_sphericity_free6.374
r_dihedral_angle_1_deg5.951
r_scangle_it3.701
r_sphericity_bonded3.239
r_mcangle_it2.792
r_scbond_it2.514
r_mcbond_it1.991
r_mcbond_other1.79
r_rigid_bond_restr1.301
r_angle_refined_deg1.298
r_angle_other_deg0.74
r_nbd_refined0.223
r_symmetry_vdw_other0.206
r_nbd_other0.166
r_symmetry_hbond_refined0.163
r_metal_ion_refined0.162
r_xyhbond_nbd_refined0.094
r_nbtor_other0.085
r_chiral_restr0.084
r_symmetry_vdw_refined0.084
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1843
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms12

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
ARP/wARPmodel building
PDB_EXTRACTdata extraction
MolProbitymodel building
SCA2STRUCTUREphasing