X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H1Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Sample preincubated with 2 mM copper(II) acetate. Reservoir consisting of 20 mM MgCl2, 0.1 M HEPES pH 7.5, 22% polyacrylic acid 5100 sodium salt.
Crystal Properties
Matthews coefficientSolvent content
2.2946.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.3α = 75.86
b = 49.11β = 88.38
c = 53.96γ = 76.31
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.350MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.3731.0891.40.0510.99818.23.982114
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.3984.20.2870.8633.2

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 REPLACEMENTTHROUGHOUT6H1Z1.3727.6571213373783.430.10740.10490.1555RANDOM18.554
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]
-0.19-1.151.430.07-1.75-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.391
r_sphericity_free32.902
r_sphericity_bonded17.367
r_dihedral_angle_4_deg14.377
r_dihedral_angle_3_deg12.051
r_dihedral_angle_1_deg6.824
r_rigid_bond_restr4.728
r_mcangle_it2.418
r_mcbond_it2.023
r_angle_refined_deg1.992
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.391
r_sphericity_free32.902
r_sphericity_bonded17.367
r_dihedral_angle_4_deg14.377
r_dihedral_angle_3_deg12.051
r_dihedral_angle_1_deg6.824
r_rigid_bond_restr4.728
r_mcangle_it2.418
r_mcbond_it2.023
r_angle_refined_deg1.992
r_mcbond_other1.981
r_angle_other_deg1.079
r_chiral_restr0.117
r_bond_refined_d0.029
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3404
Nucleic Acid Atoms
Solvent Atoms849
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
pointlessdata scaling
MOLREPphasing