X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F30 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5287Prot: 10 mg/ml prot, 25 mM borate buffer (pH 9.0), 150 mM NaCl. Prec: 0.04 M potassium dihydrogen phosphate, 16 % w/v PEG 8000, 20 % glycerol. Vprot/Vprec=1/1
Crystal Properties
Matthews coefficientSolvent content
2.0740.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.78α = 90
b = 95.42β = 100.66
c = 107γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97625ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1249940.0711.92.9124334
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)
122.15970.662.2

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 REPLACEMENTFREE R-VALUE5F30249118269606394.290.188320.185520.24396RANDOM39.521
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]
2.260.07-1.93-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.191
r_dihedral_angle_4_deg18.148
r_dihedral_angle_3_deg15.2
r_dihedral_angle_1_deg7.589
r_long_range_B_refined6.421
r_mcangle_it4.114
r_scbond_it3.686
r_mcbond_it3.041
r_angle_refined_deg1.764
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.191
r_dihedral_angle_4_deg18.148
r_dihedral_angle_3_deg15.2
r_dihedral_angle_1_deg7.589
r_long_range_B_refined6.421
r_mcangle_it4.114
r_scbond_it3.686
r_mcbond_it3.041
r_angle_refined_deg1.764
r_chiral_restr0.119
r_bond_refined_d0.015
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14504
Nucleic Acid Atoms
Solvent Atoms513
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling