X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DYL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.2293.1519% PEG3350, 0.15 M ammonium acetate, 0.1 M tris, pH 8.2
Crystal Properties
Matthews coefficientSolvent content
2.3347.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.651α = 90
b = 69.934β = 119.36
c = 73.763γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.1547.3399.90.1010.1130.050.996105.335192
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2799.90.9060.9061.020.460.6590.75.1

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 REPLACEMENTTHROUGHOUT2dyl2.1547.3333542163099.920.20530.20360.2389RANDOM62.631
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]
3.823.1-4.17-1.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.051
r_dihedral_angle_4_deg17.549
r_dihedral_angle_3_deg15.622
r_dihedral_angle_1_deg6.658
r_angle_refined_deg1.336
r_angle_other_deg1.016
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.051
r_dihedral_angle_4_deg17.549
r_dihedral_angle_3_deg15.622
r_dihedral_angle_1_deg6.658
r_angle_refined_deg1.336
r_angle_other_deg1.016
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4514
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms108

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing