X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9.5296PROTEIN SOLUTION: 10 MG/ML PROTEIN, 25 MM BORATE BUFFER (PH 9.5). PRECIPITANT SOLUTION: 0.025 M AMMONIUM IODIDE, 20.0 % W/V PEG 3350. VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K
Crystal Properties
Matthews coefficientSolvent content
2.4349.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.82α = 90
b = 159.45β = 97.77
c = 91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.900SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
123093.70.1550.99611.56124180
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0594.50.8610.7642.356

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 REPLACEMENTTHROUGHOUT5F30230118078610293.660.157840.155730.19841RANDOM21.175
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]
0.95-0.47-1.020.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.275
r_dihedral_angle_4_deg18.746
r_dihedral_angle_3_deg14.593
r_dihedral_angle_1_deg7.322
r_long_range_B_refined5.367
r_scbond_it2.908
r_mcangle_it2.344
r_angle_refined_deg2.018
r_mcbond_it1.652
r_chiral_restr0.143
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.275
r_dihedral_angle_4_deg18.746
r_dihedral_angle_3_deg14.593
r_dihedral_angle_1_deg7.322
r_long_range_B_refined5.367
r_scbond_it2.908
r_mcangle_it2.344
r_angle_refined_deg2.018
r_mcbond_it1.652
r_chiral_restr0.143
r_bond_refined_d0.019
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14572
Nucleic Acid Atoms
Solvent Atoms919
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing