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 = 136.1α = 90
b = 300.82β = 113.06
c = 144.82γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-08-14MSINGLE 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
12.33098.90.05513.747265946746022
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)
12.32.499.40.522.7

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 REPLACEMENTTHROUGHOUT1RYP2.3154674604440872337398.990.2090.206680.20570.22542RANDOM58.986
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]
2.23-0.83-4.892.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.721
r_sphericity_free25.135
r_sphericity_bonded16.642
r_dihedral_angle_3_deg13.514
r_dihedral_angle_4_deg12.751
r_dihedral_angle_1_deg4.991
r_long_range_B_refined2.823
r_long_range_B_other2.715
r_mcangle_it2.286
r_mcangle_other2.286
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.721
r_sphericity_free25.135
r_sphericity_bonded16.642
r_dihedral_angle_3_deg13.514
r_dihedral_angle_4_deg12.751
r_dihedral_angle_1_deg4.991
r_long_range_B_refined2.823
r_long_range_B_other2.715
r_mcangle_it2.286
r_mcangle_other2.286
r_scangle_other1.969
r_mcbond_other1.774
r_mcbond_it1.773
r_scbond_it1.662
r_scbond_other1.662
r_rigid_bond_restr0.91
r_angle_refined_deg0.836
r_angle_other_deg0.69
r_chiral_restr0.048
r_bond_refined_d0.004
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 Atoms49364
Nucleic Acid Atoms
Solvent Atoms1604
Heterogen Atoms181

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing