X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NYRPDB ENTRY 2NYR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.522% PEG3350, 0.1 M HEPES PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.957

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.32α = 90
b = 87.32β = 90
c = 314.57γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
13.35099.90.339.110114772
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)
13.33.41001.262.410.4

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 2NYR3.348.411088159599.870.211730.209340.25437RANDOM67.559
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]
0.650.320.65-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.382
r_dihedral_angle_4_deg17.426
r_dihedral_angle_3_deg17.185
r_dihedral_angle_1_deg6.864
r_mcangle_it3.417
r_scbond_it2.098
r_mcbond_it2.009
r_mcbond_other2.009
r_angle_refined_deg1.687
r_angle_other_deg1.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.382
r_dihedral_angle_4_deg17.426
r_dihedral_angle_3_deg17.185
r_dihedral_angle_1_deg6.864
r_mcangle_it3.417
r_scbond_it2.098
r_mcbond_it2.009
r_mcbond_other2.009
r_angle_refined_deg1.687
r_angle_other_deg1.164
r_chiral_restr0.103
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.004
r_gen_planes_other0.003
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_it
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 Atoms4125
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing