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 = 134.58α = 90
b = 299.75β = 112.52
c = 144.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-05-13MSINGLE 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
12.83099.40.06315.425929225773622
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)
12.82.999.40.4353.3

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 REPLACEMENTTHROUGHOUT1RYP2.8152577362448491288799.530.2040.202530.200990.23148RANDOM62.612
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]
5.3-3.25-6.311.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.206
r_sphericity_free32.656
r_sphericity_bonded18.296
r_dihedral_angle_3_deg13.958
r_dihedral_angle_4_deg13.505
r_dihedral_angle_1_deg5.202
r_long_range_B_refined4.52
r_long_range_B_other4.514
r_mcangle_it3.963
r_mcangle_other3.963
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.206
r_sphericity_free32.656
r_sphericity_bonded18.296
r_dihedral_angle_3_deg13.958
r_dihedral_angle_4_deg13.505
r_dihedral_angle_1_deg5.202
r_long_range_B_refined4.52
r_long_range_B_other4.514
r_mcangle_it3.963
r_mcangle_other3.963
r_scangle_other3.588
r_mcbond_it2.976
r_mcbond_other2.976
r_scbond_it2.838
r_scbond_other2.838
r_rigid_bond_restr1.143
r_angle_refined_deg0.852
r_angle_other_deg0.67
r_chiral_restr0.049
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 Atoms49370
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms12

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing