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 = 135.56α = 90
b = 299.58β = 112.81
c = 144.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-09-22MSINGLE 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
12.83098.90.1038.226091225804222

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 1RYP2.8152580422451391290398.990.1960.194550.22354RANDOM64.5
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]
3.05-1.38-6.543
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.73
r_sphericity_free29.41
r_sphericity_bonded16.197
r_dihedral_angle_3_deg15.031
r_dihedral_angle_4_deg14.804
r_dihedral_angle_1_deg5.266
r_long_range_B_refined4.367
r_long_range_B_other4.359
r_mcangle_it4.013
r_mcangle_other4.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.73
r_sphericity_free29.41
r_sphericity_bonded16.197
r_dihedral_angle_3_deg15.031
r_dihedral_angle_4_deg14.804
r_dihedral_angle_1_deg5.266
r_long_range_B_refined4.367
r_long_range_B_other4.359
r_mcangle_it4.013
r_mcangle_other4.013
r_scangle_other3.476
r_mcbond_it2.971
r_mcbond_other2.971
r_scbond_it2.734
r_scbond_other2.734
r_rigid_bond_restr1.175
r_angle_refined_deg0.921
r_angle_other_deg0.834
r_chiral_restr0.052
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms49174
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms285

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing