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, 100 mM MES, 13% MPD, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6966.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.15α = 90
b = 300.35β = 112.48
c = 144.83γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-07-06MSINGLE 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
12.74097.20.0613.252.728927728117722
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)
12.72.898.20.4981.83

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 REPLACEMENTTHROUGHOUT1RYP2.7152811772671181405997.340.1980.193790.192580.21689RANDOM58.118
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]
4.38-3.89-6.863.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free45.882
r_dihedral_angle_2_deg36.362
r_dihedral_angle_3_deg17.62
r_dihedral_angle_4_deg16.709
r_sphericity_bonded9.074
r_dihedral_angle_1_deg6
r_angle_refined_deg0.993
r_rigid_bond_restr0.924
r_angle_other_deg0.727
r_chiral_restr0.057
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free45.882
r_dihedral_angle_2_deg36.362
r_dihedral_angle_3_deg17.62
r_dihedral_angle_4_deg16.709
r_sphericity_bonded9.074
r_dihedral_angle_1_deg6
r_angle_refined_deg0.993
r_rigid_bond_restr0.924
r_angle_other_deg0.727
r_chiral_restr0.057
r_bond_refined_d0.005
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 Atoms49296
Nucleic Acid Atoms
Solvent Atoms488
Heterogen Atoms94

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing