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 = 134.69α = 90
b = 299.69β = 112.88
c = 144.45γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELPSI PILATUS 6M2011-04-11MSINGLE 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
12.53093.80.09410.453.436255534007722
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)
12.52.689.10.4322.3

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 REPLACEMENTTHROUGHOUT1RYP2.5153400773230731700493.880.240.238760.237990.24946RANDOM36.342
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]
5.37-4.37-7.823.17
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free98.962
r_dihedral_angle_2_deg35.529
r_sphericity_bonded18.464
r_dihedral_angle_3_deg15.724
r_dihedral_angle_4_deg15.674
r_rigid_bond_restr6.254
r_dihedral_angle_1_deg5.489
r_angle_refined_deg0.938
r_angle_other_deg0.734
r_chiral_restr0.053
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free98.962
r_dihedral_angle_2_deg35.529
r_sphericity_bonded18.464
r_dihedral_angle_3_deg15.724
r_dihedral_angle_4_deg15.674
r_rigid_bond_restr6.254
r_dihedral_angle_1_deg5.489
r_angle_refined_deg0.938
r_angle_other_deg0.734
r_chiral_restr0.053
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 Atoms925
Heterogen Atoms212

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing