X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYPpdb entry 1RYP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8293100 mM MES, 12% MPD, 20 mM MgAc2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.766.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.42α = 90
b = 300.42β = 112.83
c = 143.93γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-02-02MSINGLE 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
12.73099.10.09811.328951628691022
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)
12.72.898.70.5962.7

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 REPLACEMENTTHROUGHOUTpdb entry 1RYP2.7152869102725641434699.230.2240.21830.217170.23955RANDOM54.447
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]
2.18-0.79-5.662.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.602
r_sphericity_free22.807
r_sphericity_bonded20.85
r_dihedral_angle_3_deg13.128
r_dihedral_angle_4_deg9.097
r_dihedral_angle_1_deg3.975
r_rigid_bond_restr1.205
r_angle_refined_deg0.832
r_chiral_restr0.056
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.602
r_sphericity_free22.807
r_sphericity_bonded20.85
r_dihedral_angle_3_deg13.128
r_dihedral_angle_4_deg9.097
r_dihedral_angle_1_deg3.975
r_rigid_bond_restr1.205
r_angle_refined_deg0.832
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49538
Nucleic Acid Atoms
Solvent Atoms1340
Heterogen Atoms36

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing