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 = 135.2α = 90
b = 299.25β = 113.01
c = 144.85γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-02-09MSINGLE 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
133097.50.09810.921103620576022
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)
133.199.40.4693.1

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 1RYP3152057591954711028897.620.182680.180840.2178RANDOM62.141
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]
4.42-0.46-5.931.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.283
r_sphericity_free29.447
r_sphericity_bonded17.328
r_dihedral_angle_3_deg13.681
r_dihedral_angle_4_deg13.21
r_dihedral_angle_1_deg5.15
r_long_range_B_refined3.857
r_long_range_B_other3.845
r_mcangle_it3.35
r_mcangle_other3.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.283
r_sphericity_free29.447
r_sphericity_bonded17.328
r_dihedral_angle_3_deg13.681
r_dihedral_angle_4_deg13.21
r_dihedral_angle_1_deg5.15
r_long_range_B_refined3.857
r_long_range_B_other3.845
r_mcangle_it3.35
r_mcangle_other3.35
r_scangle_other3.046
r_mcbond_it2.504
r_mcbond_other2.504
r_scbond_it2.44
r_scbond_other2.44
r_angle_refined_deg0.852
r_rigid_bond_restr0.78
r_angle_other_deg0.704
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 Atoms49376
Nucleic Acid Atoms
Solvent Atoms221
Heterogen Atoms179

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing