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Human Topoisomerase II Beta ATPase AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M PCTP (pH 7.0), 25 % w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.46 49.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.021 α = 90 b = 84.021 β = 90 c = 127.091 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2021-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9796 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 59.42 100 1 23.3 48 36646
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 99.9 0.568 1.2 50.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1ZXM 1.9 59.412 36567 1769 99.975 0.195 0.1927 0.2318 0.1992 42.104
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] 0.224 0.224 -0.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.076 r_dihedral_angle_4_deg 20.206 r_dihedral_angle_3_deg 15.733 r_lrange_other 8.293 r_lrange_it 8.288 r_dihedral_angle_1_deg 7.428 r_scangle_it 6.94 r_scangle_other 6.938 r_scbond_it 4.621 r_scbond_other 4.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.076 r_dihedral_angle_4_deg 20.206 r_dihedral_angle_3_deg 15.733 r_lrange_other 8.293 r_lrange_it 8.288 r_dihedral_angle_1_deg 7.428 r_scangle_it 6.94 r_scangle_other 6.938 r_scbond_it 4.621 r_scbond_other 4.62 r_mcangle_it 4.541 r_mcangle_other 4.54 r_mcbond_other 3.644 r_mcbond_it 3.642 r_angle_refined_deg 1.729 r_angle_other_deg 1.343 r_chiral_restr_other 0.369 r_nbd_refined 0.211 r_nbd_other 0.197 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.137 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3034 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data reduction pointless data scaling Coot model building MolProbity model building Aimless data scaling PHASER phasing MOLREP phasing