X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8SZR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6291200 mM Lithium sulfate, 100 mM MES pH 6, 20% (w/v) PEG 4000; 5 mM ADP and 50 mM magnesium chloride in protein solution
Crystal Properties
Matthews coefficientSolvent content
2.7855.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.1α = 90
b = 122.26β = 90
c = 349.18γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97624DiamondI03

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
12.6261.1399.70.0620.0640.018121.812.876541
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)
12.622.6799.41.3981.450.3820.81514

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.6259.62176498376999.5520.2220.21940.2736RANDOM87.946
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]
5.65-3.047-2.602
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.486
r_dihedral_angle_6_deg12.623
r_lrange_other9.925
r_lrange_it9.924
r_mcangle_it6.778
r_mcangle_other6.778
r_scangle_it6.631
r_scangle_other6.631
r_dihedral_angle_1_deg6.123
r_mcbond_it4.251
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.486
r_dihedral_angle_6_deg12.623
r_lrange_other9.925
r_lrange_it9.924
r_mcangle_it6.778
r_mcangle_other6.778
r_scangle_it6.631
r_scangle_other6.631
r_dihedral_angle_1_deg6.123
r_mcbond_it4.251
r_mcbond_other4.246
r_dihedral_angle_2_deg4.177
r_scbond_it4.014
r_scbond_other4.014
r_angle_refined_deg0.877
r_angle_other_deg0.296
r_nbd_refined0.203
r_symmetry_nbd_other0.182
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.144
r_nbd_other0.109
r_symmetry_xyhbond_nbd_refined0.081
r_symmetry_nbtor_other0.073
r_symmetry_nbd_refined0.067
r_symmetry_xyhbond_nbd_other0.047
r_chiral_restr0.042
r_chiral_restr_other0.026
r_dihedral_angle_other_2_deg0.012
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13583
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms165

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing