X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DNZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1M Bis-tris, 1.45M (NH4)2SO4, 0.1M NaCl, 0.5M Sodium fluoride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.766.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.864α = 90
b = 143.279β = 90
c = 172.513γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTCmirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.95099.70.1410.097152.358819586461139.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.9599.60.5660.5673.582.22886

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DNZ2.9141.575602655617297099.270.1850.181640.24919RANDOM36.352
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]
0.02-0.090.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.745
r_dihedral_angle_3_deg17.972
r_dihedral_angle_4_deg17.691
r_dihedral_angle_1_deg6.744
r_scangle_it3.184
r_scbond_it1.887
r_angle_refined_deg1.719
r_mcangle_it1.154
r_mcbond_it0.583
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.745
r_dihedral_angle_3_deg17.972
r_dihedral_angle_4_deg17.691
r_dihedral_angle_1_deg6.744
r_scangle_it3.184
r_scbond_it1.887
r_angle_refined_deg1.719
r_mcangle_it1.154
r_mcbond_it0.583
r_chiral_restr0.106
r_bond_refined_d0.017
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12090
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms319

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling