X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y8NPDB entry 1Y8N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.9M ammonium sulfate, 4% polyethylene glycol 400, 100mM potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2144.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.616α = 90
b = 68.743β = 100.1
c = 81.554γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrrors2008-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.98APS19-ID

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
125099.60.05623.44.152354
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)
22.031000.6652.44.22631

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1Y8N249.2249635266899.370.187710.184880.24016RANDOM41.96
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]
-0.21-0.21.08-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.923
r_dihedral_angle_4_deg21.24
r_dihedral_angle_3_deg16.176
r_dihedral_angle_1_deg5.851
r_scangle_it4.52
r_scbond_it3.165
r_mcangle_it1.842
r_angle_refined_deg1.831
r_mcbond_it1.387
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.923
r_dihedral_angle_4_deg21.24
r_dihedral_angle_3_deg16.176
r_dihedral_angle_1_deg5.851
r_scangle_it4.52
r_scbond_it3.165
r_mcangle_it1.842
r_angle_refined_deg1.831
r_mcbond_it1.387
r_nbtor_refined0.317
r_nbd_refined0.225
r_symmetry_hbond_refined0.224
r_symmetry_vdw_refined0.163
r_xyhbond_nbd_refined0.139
r_chiral_restr0.135
r_bond_refined_d0.021
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5737
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing