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 = 135.96α = 90
b = 301.96β = 113.14
c = 145.05γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-11-30MSINGLE 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
12.93090.30.08912.623713321413122
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)
12.9392.70.5432.5

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 REPLACEMENTTHROUGHOUT1RYP2.9152141312034241070790.430.1830.180530.17910.20786RANDOM57.943
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]
3.16-0.64-4.861.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.961
r_sphericity_free26.297
r_sphericity_bonded14.245
r_dihedral_angle_3_deg13.766
r_dihedral_angle_4_deg12.816
r_dihedral_angle_1_deg4.971
r_long_range_B_refined3.299
r_long_range_B_other3.286
r_mcangle_it2.775
r_mcangle_other2.775
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.961
r_sphericity_free26.297
r_sphericity_bonded14.245
r_dihedral_angle_3_deg13.766
r_dihedral_angle_4_deg12.816
r_dihedral_angle_1_deg4.971
r_long_range_B_refined3.299
r_long_range_B_other3.286
r_mcangle_it2.775
r_mcangle_other2.775
r_scangle_other2.63
r_scbond_it2.116
r_scbond_other2.116
r_mcbond_it2.088
r_mcbond_other2.088
r_angle_refined_deg0.842
r_rigid_bond_restr0.8
r_angle_other_deg0.784
r_chiral_restr0.048
r_bond_refined_d0.004
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49366
Nucleic Acid Atoms
Solvent Atoms329
Heterogen Atoms101

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing