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, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
3.6766.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.77α = 90
b = 301.43β = 112.84
c = 144.14γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-03-07MSINGLE 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
12.53097.40.05916.73.4364225354755
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)
12.52.698.30.5322.7

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 REPLACEMENTTHROUGHOUT1RYP2.5153370171773897.490.206970.206060.22431RANDOM54.812
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]
2.9-1.44-5.012.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.2
r_sphericity_free30.687
r_dihedral_angle_3_deg14.188
r_dihedral_angle_4_deg14.112
r_dihedral_angle_1_deg5.173
r_sphericity_bonded4.064
r_long_range_B_refined2.231
r_long_range_B_other2.13
r_mcangle_it1.624
r_mcangle_other1.624
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.2
r_sphericity_free30.687
r_dihedral_angle_3_deg14.188
r_dihedral_angle_4_deg14.112
r_dihedral_angle_1_deg5.173
r_sphericity_bonded4.064
r_long_range_B_refined2.231
r_long_range_B_other2.13
r_mcangle_it1.624
r_mcangle_other1.624
r_scangle_other1.472
r_scbond_it1.359
r_scbond_other1.359
r_mcbond_it1.327
r_mcbond_other1.327
r_rigid_bond_restr1.229
r_angle_refined_deg0.849
r_angle_other_deg0.667
r_chiral_restr0.052
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 Atoms49333
Nucleic Acid Atoms
Solvent Atoms1198
Heterogen Atoms10

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement