X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.620% PEG3350, 0.1 M HEPES PH 7.6
Crystal Properties
Matthews coefficientSolvent content
2.857

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.19α = 90
b = 87.19β = 90
c = 313.87γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-04-17MSINGLE 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
12.85099.60.2510.610.5182921.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.91001.311.1

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 2NYR2.819.871737591599.550.210710.208030.26138RANDOM70.386
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]
0.420.210.42-1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.574
r_dihedral_angle_3_deg16.714
r_dihedral_angle_4_deg13.471
r_dihedral_angle_1_deg6.102
r_mcangle_it4.772
r_scbond_it3.49
r_mcbond_it2.925
r_mcbond_other2.924
r_angle_refined_deg1.69
r_angle_other_deg1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.574
r_dihedral_angle_3_deg16.714
r_dihedral_angle_4_deg13.471
r_dihedral_angle_1_deg6.102
r_mcangle_it4.772
r_scbond_it3.49
r_mcbond_it2.925
r_mcbond_other2.924
r_angle_refined_deg1.69
r_angle_other_deg1.13
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
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 Atoms4164
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing