X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DD2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52915% [w/v] PEG-6000, 2.5% v/v (+/-)-2-Methyl-2,4-pentanediol, 50 mM HEPES
Crystal Properties
Matthews coefficientSolvent content
3.1460.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.663α = 90
b = 139.166β = 90
c = 44.511γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2015-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.85942.396.90.1390.13922.65.6406853.5
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)
11.8591.985.60.4172.915.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3DD21.85942.33.540248251595.80.1910.1890.2236RANDOM34.446
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]
-3.145.93-2.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.898
r_dihedral_angle_3_deg15.055
r_dihedral_angle_4_deg14.114
r_dihedral_angle_1_deg7.7
r_mcangle_it3.831
r_mcbond_it2.622
r_mcbond_other2.621
r_angle_refined_deg1.431
r_angle_other_deg0.798
r_chiral_restr0.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.898
r_dihedral_angle_3_deg15.055
r_dihedral_angle_4_deg14.114
r_dihedral_angle_1_deg7.7
r_mcangle_it3.831
r_mcbond_it2.622
r_mcbond_other2.621
r_angle_refined_deg1.431
r_angle_other_deg0.798
r_chiral_restr0.149
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2321
Nucleic Acid Atoms535
Solvent Atoms163
Heterogen Atoms82

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing