2E6U

Crystal structure of hypothetical protein PH1109 from Pyrococcus horikoshii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529840% (v/v) PEG 300, 0.1M Cacodylate buffer pH6.5, 0.2M Calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9758.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.563α = 90
b = 69.563β = 90
c = 142.606γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2004-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

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
11.8501000.07323.313.61964819648-3-321.426
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)
11.81.861000.4586.612.81905

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 DIFFRACTIONSADTHROUGHOUT1.820185659991000.206680.205360.23305RANDOM23.373
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]
0.510.260.51-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.486
r_dihedral_angle_4_deg26.182
r_dihedral_angle_3_deg16.069
r_dihedral_angle_1_deg5.462
r_scangle_it4.11
r_scbond_it2.676
r_mcangle_it1.651
r_angle_refined_deg1.622
r_mcbond_it0.952
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.486
r_dihedral_angle_4_deg26.182
r_dihedral_angle_3_deg16.069
r_dihedral_angle_1_deg5.462
r_scangle_it4.11
r_scbond_it2.676
r_mcangle_it1.651
r_angle_refined_deg1.622
r_mcbond_it0.952
r_nbtor_refined0.311
r_metal_ion_refined0.289
r_symmetry_vdw_refined0.203
r_nbd_refined0.202
r_chiral_restr0.152
r_xyhbond_nbd_refined0.13
r_symmetry_hbond_refined0.114
r_bond_refined_d0.013
r_symmetry_metal_ion_refined0.01
r_gen_planes_refined0.006
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1155
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXEmodel building