X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72932.5 M sodium formate, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.7655.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.29α = 90
b = 70.41β = 133.61
c = 106.67γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2019-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.9795RRCAT INDUS-2PX-BL21

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.939.8995.90.9916.162.896132941.24
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9296.60.651.842.73

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 REPLACEMENTTHROUGHOUT5YIC1.939.8958262306796.340.224480.222250.26126RANDOM51.907
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]
1.551.21-5.030.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.682
r_dihedral_angle_4_deg21.774
r_dihedral_angle_3_deg14.629
r_long_range_B_refined7.676
r_long_range_B_other7.659
r_dihedral_angle_1_deg7.502
r_angle_refined_deg1.309
r_angle_other_deg1.08
r_scangle_other0.985
r_mcangle_it0.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.682
r_dihedral_angle_4_deg21.774
r_dihedral_angle_3_deg14.629
r_long_range_B_refined7.676
r_long_range_B_other7.659
r_dihedral_angle_1_deg7.502
r_angle_refined_deg1.309
r_angle_other_deg1.08
r_scangle_other0.985
r_mcangle_it0.722
r_mcangle_other0.722
r_scbond_it0.586
r_scbond_other0.586
r_mcbond_it0.405
r_mcbond_other0.405
r_chiral_restr0.045
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5189
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms567

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing