X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829320 MM MGAC2, 13% MPD, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 6.8
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.6α = 90
b = 300.05β = 112.77
c = 145.62γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
12.93095.80.0879.823647822654622
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)
12.9397.20.5392.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RYP2.9152265462152181132895.870.1770.173660.171660.21169RANDOM75.235
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]
2.430.07-94.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.324
r_sphericity_free34.147
r_sphericity_bonded22.254
r_dihedral_angle_3_deg14.416
r_dihedral_angle_4_deg14.247
r_long_range_B_refined5.361
r_long_range_B_other5.358
r_dihedral_angle_1_deg5.15
r_mcangle_it4.64
r_mcangle_other4.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.324
r_sphericity_free34.147
r_sphericity_bonded22.254
r_dihedral_angle_3_deg14.416
r_dihedral_angle_4_deg14.247
r_long_range_B_refined5.361
r_long_range_B_other5.358
r_dihedral_angle_1_deg5.15
r_mcangle_it4.64
r_mcangle_other4.64
r_scangle_other4.357
r_mcbond_it3.433
r_mcbond_other3.433
r_scbond_it3.364
r_scbond_other3.364
r_rigid_bond_restr1.186
r_angle_refined_deg0.892
r_angle_other_deg0.802
r_chiral_restr0.051
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49296
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms312

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing