X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.829820 mM MgAC2, 13% MPD, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135α = 90
b = 301.73β = 113.06
c = 144.02γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-07-19MSINGLE 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
12.73094.70.077123.1274146
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)
12.72.8980.5282.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RYP2.7152604371370894.830.207640.206420.23083RANDOM55.758
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]
3.56-2.23-4.341.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.764
r_sphericity_free31.873
r_sphericity_bonded16.107
r_dihedral_angle_4_deg14.61
r_dihedral_angle_3_deg14.449
r_dihedral_angle_1_deg5.217
r_long_range_B_refined3.354
r_long_range_B_other3.322
r_mcangle_it2.845
r_mcangle_other2.845
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.764
r_sphericity_free31.873
r_sphericity_bonded16.107
r_dihedral_angle_4_deg14.61
r_dihedral_angle_3_deg14.449
r_dihedral_angle_1_deg5.217
r_long_range_B_refined3.354
r_long_range_B_other3.322
r_mcangle_it2.845
r_mcangle_other2.845
r_scangle_other2.607
r_scbond_it2.143
r_scbond_other2.143
r_mcbond_it2.142
r_mcbond_other2.142
r_rigid_bond_restr1.411
r_angle_refined_deg0.859
r_angle_other_deg0.681
r_chiral_restr0.05
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49376
Nucleic Acid Atoms
Solvent Atoms603
Heterogen Atoms10

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement