X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KNB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52910.1 M MMT Buffer, 25% PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.1542.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.259α = 90
b = 99.619β = 100.26
c = 113.549γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.955.961000.150.1750.0890.9734.43.825128
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.92.981001.1171.2960.6490.6523.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT3.155.8719502100499.890.239030.2340.33672RANDOM93.976
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]
2.540.460.9-3.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.245
r_dihedral_angle_3_deg22.964
r_dihedral_angle_4_deg18.843
r_dihedral_angle_1_deg12.095
r_long_range_B_refined3.644
r_long_range_B_other3.644
r_mcangle_it2.192
r_mcangle_other2.192
r_scangle_other1.632
r_angle_refined_deg1.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.245
r_dihedral_angle_3_deg22.964
r_dihedral_angle_4_deg18.843
r_dihedral_angle_1_deg12.095
r_long_range_B_refined3.644
r_long_range_B_other3.644
r_mcangle_it2.192
r_mcangle_other2.192
r_scangle_other1.632
r_angle_refined_deg1.371
r_mcbond_it1.272
r_mcbond_other1.272
r_angle_other_deg1.053
r_scbond_it0.908
r_scbond_other0.907
r_chiral_restr0.05
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms8946
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing