X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7P4K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729325% PEG Smear High, 0.1M PIPES pH 7.0, 0.1M magnesium formate, 0.1M rubidium chloride
Crystal Properties
Matthews coefficientSolvent content
1.9637.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.924α = 90
b = 80.312β = 90
c = 89.084γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.344.5499.60.0750.0820.0320.99810.76.480739
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)
11.31.3393.31.1491.2630.5170.5735.8

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 REPLACEMENTTHROUGHOUT1.344.5476583409199.610.163710.162790.18041RANDOM18.14
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]
0.22-0.820.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.165
r_dihedral_angle_2_deg7.199
r_dihedral_angle_1_deg6.871
r_long_range_B_refined5.262
r_long_range_B_other5.262
r_scangle_other3.975
r_scbond_it2.733
r_scbond_other2.732
r_mcangle_other2.378
r_mcangle_it2.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.165
r_dihedral_angle_2_deg7.199
r_dihedral_angle_1_deg6.871
r_long_range_B_refined5.262
r_long_range_B_other5.262
r_scangle_other3.975
r_scbond_it2.733
r_scbond_other2.732
r_mcangle_other2.378
r_mcangle_it2.373
r_angle_refined_deg1.926
r_mcbond_it1.624
r_mcbond_other1.603
r_angle_other_deg0.655
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
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 Atoms2553
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing