X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293.1525% PEG3350, 0.1 M ammonium acetate, 0.1 M tris, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.2845.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.07α = 90
b = 69.24β = 117.92
c = 72.25γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
12.261.8399.90.070.0780.0340.99810.2532046
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)
12.22.3299.90.770.770.8590.3750.740.94.9

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 REPLACEMENTTHROUGHOUT2dyl2.261.8330353164699.770.20950.20740.251RANDOM65.103
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]
1.87-2.242.42-1.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.194
r_dihedral_angle_4_deg19.101
r_dihedral_angle_3_deg15.123
r_dihedral_angle_1_deg6.556
r_angle_refined_deg1.472
r_angle_other_deg1.076
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.194
r_dihedral_angle_4_deg19.101
r_dihedral_angle_3_deg15.123
r_dihedral_angle_1_deg6.556
r_angle_refined_deg1.472
r_angle_other_deg1.076
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4425
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms104

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing