X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DYR2DYR and 1HRC
experimental modelPDB 1HRC2DYR and 1HRC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE827715mM sodium phosphate, pH 8.0, 0.7% fluorinated octylmaltoside, 0.2% decylmaltoside, 3% ethylene glycol, 5% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.5565.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.29α = 90
b = 183.872β = 102.12
c = 148.929γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2015-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
125099.50.0960.1050.0448.84.9397399
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0299.50.5990.6233.79885

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2DYR and 1HRC2403773381999099.40.16860.16650.2074RANDOM48.152
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]
-1.780.243.62-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.558
r_dihedral_angle_4_deg16.908
r_dihedral_angle_3_deg16.469
r_sphericity_bonded7.54
r_dihedral_angle_1_deg6.584
r_scbond_it4.651
r_mcangle_it4.485
r_mcbond_it3.204
r_angle_refined_deg2.205
r_chiral_restr0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.558
r_dihedral_angle_4_deg16.908
r_dihedral_angle_3_deg16.469
r_sphericity_bonded7.54
r_dihedral_angle_1_deg6.584
r_scbond_it4.651
r_mcangle_it4.485
r_mcbond_it3.204
r_angle_refined_deg2.205
r_chiral_restr0.15
r_bond_refined_d0.026
r_gen_planes_refined0.024
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms30158
Nucleic Acid Atoms
Solvent Atoms2237
Heterogen Atoms2183

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing