X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OYJPDB ENTRY 1OYJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PEG
Crystal Properties
Matthews coefficientSolvent content
2.449.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.375α = 90
b = 91.375β = 90
c = 111.83γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.7570.7198.90.054248045-3
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)
11.751.781000.524.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1OYJ1.7570.7145117240098.90.1970.1940.243RANDOM26.71
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]
0.220.22-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.227
r_dihedral_angle_4_deg17.161
r_dihedral_angle_3_deg15.984
r_dihedral_angle_1_deg10.064
r_scangle_it3.721
r_scbond_it2.411
r_angle_refined_deg1.634
r_mcangle_it1.483
r_mcbond_it0.942
r_xyhbond_nbd_refined0.454
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.227
r_dihedral_angle_4_deg17.161
r_dihedral_angle_3_deg15.984
r_dihedral_angle_1_deg10.064
r_scangle_it3.721
r_scbond_it2.411
r_angle_refined_deg1.634
r_mcangle_it1.483
r_mcbond_it0.942
r_xyhbond_nbd_refined0.454
r_nbtor_refined0.313
r_symmetry_hbond_refined0.274
r_symmetry_vdw_refined0.253
r_nbd_refined0.219
r_chiral_restr0.128
r_bond_refined_d0.015
r_gen_planes_refined0.007
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_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 Atoms3622
Nucleic Acid Atoms
Solvent Atoms430
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
HKLdata reduction
SCALEPACKdata scaling
PHASERphasing