X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZHZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2944.4 M sodium formate (HCOONa)
Crystal Properties
Matthews coefficientSolvent content
3.160.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 247.531α = 90
b = 110.683β = 129.46
c = 159.285γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C0.772ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.115099.10.0720.99810.523.38373419
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.112.241.470.484

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 SYNTHESISTHROUGHOUT6ZHZ2.2847.92143514748899.870.186970.183840.24656RANDOM55.665
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]
-1.26-0.571.160.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.127
r_dihedral_angle_4_deg20.192
r_dihedral_angle_3_deg19.266
r_long_range_B_refined8.235
r_long_range_B_other8.227
r_dihedral_angle_1_deg7.314
r_scangle_other4.413
r_mcangle_it4.243
r_mcangle_other4.243
r_scbond_it3.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.127
r_dihedral_angle_4_deg20.192
r_dihedral_angle_3_deg19.266
r_long_range_B_refined8.235
r_long_range_B_other8.227
r_dihedral_angle_1_deg7.314
r_scangle_other4.413
r_mcangle_it4.243
r_mcangle_other4.243
r_scbond_it3.145
r_scbond_other2.909
r_mcbond_it2.805
r_mcbond_other2.805
r_angle_refined_deg2.164
r_angle_other_deg1.438
r_chiral_restr0.219
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_gen_planes_other0.006
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 Atoms18604
Nucleic Acid Atoms
Solvent Atoms1355
Heterogen Atoms1095

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing