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 = 134.85α = 90
b = 301.41β = 112.97
c = 143.56γ = 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
133096.10.07511.121015420195822
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)
133.197.90.4811.9

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 REPLACEMENTTHROUGHOUT1RYP3152019581918601009896.210.1780.173360.171410.21069RANDOM74.574
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]
4.74-2.41-7.262.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.647
r_sphericity_free29.357
r_sphericity_bonded19.339
r_dihedral_angle_3_deg13.529
r_dihedral_angle_4_deg12.679
r_dihedral_angle_1_deg4.946
r_long_range_B_refined4.797
r_long_range_B_other4.79
r_mcangle_it4.254
r_mcangle_other4.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.647
r_sphericity_free29.357
r_sphericity_bonded19.339
r_dihedral_angle_3_deg13.529
r_dihedral_angle_4_deg12.679
r_dihedral_angle_1_deg4.946
r_long_range_B_refined4.797
r_long_range_B_other4.79
r_mcangle_it4.254
r_mcangle_other4.254
r_scangle_other3.87
r_mcbond_it3.176
r_mcbond_other3.176
r_scbond_it3.078
r_scbond_other3.077
r_rigid_bond_restr0.893
r_angle_refined_deg0.825
r_angle_other_deg0.683
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49364
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms9

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing