X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291precipitant containing 20% PEG3350, 0.2 M dibasic ammonium citrate. Protein mixed 1uL:1uL protein:precipitant and set as 2 uL hanging drop on glass slides
Crystal Properties
Matthews coefficientSolvent content
2.6854.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.939α = 90
b = 172.573β = 90
c = 83.297γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-06-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

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
12.194099.70.2260.2390.0760.9845.4944382
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)
12.22.2499.72.7492.9751.1140.2916.8

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 REPLACEMENTTHROUGHOUT2.1938.674390446299.470.172230.171680.22275RANDOM40.183
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]
-1.431.46-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.519
r_dihedral_angle_2_deg9.016
r_long_range_B_refined8.679
r_long_range_B_other8.678
r_dihedral_angle_1_deg7.198
r_scangle_other6.851
r_mcangle_it5.29
r_mcangle_other5.289
r_scbond_it4.73
r_scbond_other4.729
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.519
r_dihedral_angle_2_deg9.016
r_long_range_B_refined8.679
r_long_range_B_other8.678
r_dihedral_angle_1_deg7.198
r_scangle_other6.851
r_mcangle_it5.29
r_mcangle_other5.289
r_scbond_it4.73
r_scbond_other4.729
r_mcbond_it3.776
r_mcbond_other3.776
r_angle_refined_deg1.574
r_angle_other_deg0.518
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5319
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms280

Software

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