X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YRZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52920.2 M sodium acetate pH 5, 20-30% PEG-3350
Crystal Properties
Matthews coefficientSolvent content
2.2845.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.46α = 90
b = 71.4β = 94.78
c = 160.3γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2013-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.980DiamondI02

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
12.2852.1999.60.09211.14.146976
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)
12.282.3499.50.6242.34.2

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 REPLACEMENTTHROUGHOUT1yrz2.2852.1944617235899.540.195130.192220.25023RANDOM34.601
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]
1.380.83-3.411.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.905
r_dihedral_angle_4_deg13.651
r_dihedral_angle_3_deg13.198
r_dihedral_angle_1_deg6.77
r_long_range_B_other6.621
r_long_range_B_refined6.62
r_scangle_other5.066
r_mcangle_it4.474
r_mcangle_other4.473
r_scbond_it3.593
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.905
r_dihedral_angle_4_deg13.651
r_dihedral_angle_3_deg13.198
r_dihedral_angle_1_deg6.77
r_long_range_B_other6.621
r_long_range_B_refined6.62
r_scangle_other5.066
r_mcangle_it4.474
r_mcangle_other4.473
r_scbond_it3.593
r_scbond_other3.592
r_mcbond_it3.171
r_mcbond_other3.168
r_angle_refined_deg1.324
r_angle_other_deg0.911
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7723
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing