X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYPpdb entry 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 = 137.68α = 90
b = 300.99β = 112.96
c = 145.99γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-08-14MSINGLE 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
133097.90.06912.521804821346922
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)
133.1990.422.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1RYP3152134672027931067498.070.176480.174490.21444RANDOM79.627
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]
5.32-0.61-10.894.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.046
r_sphericity_free31.271
r_sphericity_bonded20.994
r_dihedral_angle_3_deg14.012
r_dihedral_angle_4_deg13.553
r_long_range_B_refined5.297
r_long_range_B_other5.295
r_dihedral_angle_1_deg4.979
r_mcangle_it4.733
r_mcangle_other4.733
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.046
r_sphericity_free31.271
r_sphericity_bonded20.994
r_dihedral_angle_3_deg14.012
r_dihedral_angle_4_deg13.553
r_long_range_B_refined5.297
r_long_range_B_other5.295
r_dihedral_angle_1_deg4.979
r_mcangle_it4.733
r_mcangle_other4.733
r_scangle_other4.258
r_mcbond_it3.545
r_mcbond_other3.545
r_scbond_it3.369
r_scbond_other3.369
r_rigid_bond_restr0.925
r_angle_refined_deg0.867
r_angle_other_deg0.78
r_chiral_restr0.049
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 Atoms49305
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms368

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing