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 = 135.81α = 90
b = 298.69β = 112.69
c = 145.7γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-03-16MSINGLE 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
12.83096.90.08210.426236325423022
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)
12.82.9980.5442.3

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 REPLACEMENTTHROUGHOUT1RYP2.8152542302415181271297.040.1910.188610.187160.21636RANDOM61.124
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]
1.91-0.67-4.492.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.036
r_sphericity_free25.327
r_sphericity_bonded16.017
r_dihedral_angle_3_deg14.084
r_dihedral_angle_4_deg13.403
r_dihedral_angle_1_deg5.028
r_long_range_B_refined3.774
r_long_range_B_other3.769
r_mcangle_it3.257
r_mcangle_other3.257
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.036
r_sphericity_free25.327
r_sphericity_bonded16.017
r_dihedral_angle_3_deg14.084
r_dihedral_angle_4_deg13.403
r_dihedral_angle_1_deg5.028
r_long_range_B_refined3.774
r_long_range_B_other3.769
r_mcangle_it3.257
r_mcangle_other3.257
r_scangle_other2.989
r_mcbond_it2.42
r_mcbond_other2.42
r_scbond_it2.345
r_scbond_other2.345
r_rigid_bond_restr0.936
r_angle_refined_deg0.865
r_angle_other_deg0.762
r_chiral_restr0.049
r_bond_refined_d0.005
r_bond_other_d0.002
r_gen_planes_refined0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49295
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms371

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing