X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529512 mg/mL protein, 20% w/v PEG 3350, 200 mM K Acetate
Crystal Properties
Matthews coefficientSolvent content
2.7154.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.192α = 90
b = 81.066β = 90
c = 136.91γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-02-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.979APS19-ID

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
12.32094.90.0710.23.624382
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)
12.32.340.246

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5VGP2.311422903118995.320.2250.222650.26844RANDOM53.827
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]
-4.52-4.088.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.514
r_dihedral_angle_3_deg17.318
r_long_range_B_refined11.335
r_long_range_B_other11.332
r_scangle_other8.132
r_dihedral_angle_4_deg8.099
r_dihedral_angle_1_deg8.089
r_mcangle_it7.371
r_mcangle_other7.371
r_scbond_it5.211
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.514
r_dihedral_angle_3_deg17.318
r_long_range_B_refined11.335
r_long_range_B_other11.332
r_scangle_other8.132
r_dihedral_angle_4_deg8.099
r_dihedral_angle_1_deg8.089
r_mcangle_it7.371
r_mcangle_other7.371
r_scbond_it5.211
r_scbond_other5.21
r_mcbond_it4.722
r_mcbond_other4.717
r_angle_refined_deg2.045
r_angle_other_deg1.251
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3334
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms212

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing