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, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.48α = 90
b = 300.28β = 112.71
c = 143.96γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-10-20MSINGLE 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
12.63098.10.06414.332202831590922

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 REPLACEMENTTHROUGHOUT1RYP2.6153159083001121579698.380.1970.193880.192580.21856RANDOM61.356
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]
2.96-2.11-5.432.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.066
r_sphericity_free27.691
r_sphericity_bonded17.215
r_dihedral_angle_3_deg14.096
r_dihedral_angle_4_deg13.631
r_dihedral_angle_1_deg5.128
r_long_range_B_refined3.369
r_long_range_B_other3.339
r_mcangle_it2.914
r_mcangle_other2.914
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.066
r_sphericity_free27.691
r_sphericity_bonded17.215
r_dihedral_angle_3_deg14.096
r_dihedral_angle_4_deg13.631
r_dihedral_angle_1_deg5.128
r_long_range_B_refined3.369
r_long_range_B_other3.339
r_mcangle_it2.914
r_mcangle_other2.914
r_scangle_other2.575
r_mcbond_it2.188
r_mcbond_other2.188
r_scbond_it2.095
r_scbond_other2.095
r_rigid_bond_restr0.904
r_angle_refined_deg0.877
r_angle_other_deg0.767
r_chiral_restr0.049
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49299
Nucleic Acid Atoms
Solvent Atoms652
Heterogen Atoms348

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing