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 = 134.8α = 90
b = 300.21β = 112.86
c = 144.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-05-13MSINGLE 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
13.13097.90.1117.719105418704222
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)
13.13.299.20.4952.4

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 REPLACEMENTTHROUGHOUT1RYP3.115187042177689935398.060.161250.159360.19654RANDOM76.031
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]
4.08-1.16-7.853.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.897
r_sphericity_free32.095
r_sphericity_bonded19.691
r_dihedral_angle_3_deg13.809
r_dihedral_angle_4_deg13.046
r_long_range_B_refined5.236
r_long_range_B_other5.231
r_dihedral_angle_1_deg5.186
r_mcangle_it4.57
r_mcangle_other4.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.897
r_sphericity_free32.095
r_sphericity_bonded19.691
r_dihedral_angle_3_deg13.809
r_dihedral_angle_4_deg13.046
r_long_range_B_refined5.236
r_long_range_B_other5.231
r_dihedral_angle_1_deg5.186
r_mcangle_it4.57
r_mcangle_other4.57
r_scangle_other4.229
r_mcbond_it3.386
r_mcbond_other3.386
r_scbond_it3.318
r_scbond_other3.318
r_rigid_bond_restr1.125
r_angle_refined_deg0.838
r_angle_other_deg0.676
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49374
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms8

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing