8XJR | pdb_00008xjr

Apo form of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TAQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2890.1M HEPES pH7.5, 1.5M Lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.8657.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.222α = 90
b = 113.206β = 90
c = 198.403γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.979SSRFBL18U1

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
11.975099.80.0870.0920.0290.9945.29.851203
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)
11.9721000.5830.6190.2030.9089.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9717.748611259299.60.196180.19380.20130.241610.2483RANDOM31.375
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]
-0.581.77-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.936
r_dihedral_angle_3_deg14.624
r_long_range_B_refined6.962
r_long_range_B_other6.682
r_dihedral_angle_1_deg5.605
r_scangle_other4.341
r_mcangle_other2.972
r_mcangle_it2.971
r_scbond_it2.717
r_scbond_other2.663
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.936
r_dihedral_angle_3_deg14.624
r_long_range_B_refined6.962
r_long_range_B_other6.682
r_dihedral_angle_1_deg5.605
r_scangle_other4.341
r_mcangle_other2.972
r_mcangle_it2.971
r_scbond_it2.717
r_scbond_other2.663
r_mcbond_it1.976
r_mcbond_other1.976
r_angle_refined_deg1.101
r_angle_other_deg0.379
r_chiral_restr0.055
r_gen_planes_refined0.005
r_bond_refined_d0.004
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 Atoms4244
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms50

Software

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