X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RYPpdb entry 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 = 134.54α = 90
b = 300.51β = 112.67
c = 144.28γ = 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
12.53098.70.06911.936336035863722
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)
12.52.698.80.512.2

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1RYP2.5153586373407051793298.80.195320.194250.21559RANDOM58.161
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]
2.9-1.4-4.961.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.791
r_sphericity_free27.559
r_sphericity_bonded15.651
r_dihedral_angle_3_deg13.75
r_dihedral_angle_4_deg13.019
r_dihedral_angle_1_deg5.06
r_long_range_B_refined2.917
r_long_range_B_other2.857
r_mcangle_it2.462
r_mcangle_other2.462
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.791
r_sphericity_free27.559
r_sphericity_bonded15.651
r_dihedral_angle_3_deg13.75
r_dihedral_angle_4_deg13.019
r_dihedral_angle_1_deg5.06
r_long_range_B_refined2.917
r_long_range_B_other2.857
r_mcangle_it2.462
r_mcangle_other2.462
r_scangle_other2.177
r_mcbond_it1.889
r_mcbond_other1.889
r_scbond_it1.835
r_scbond_other1.835
r_rigid_bond_restr0.849
r_angle_refined_deg0.828
r_angle_other_deg0.671
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 Atoms49360
Nucleic Acid Atoms
Solvent Atoms924
Heterogen Atoms12

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing