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Crystal structure of Topoisomerase V from Methanopyrus kandleri (61 kDa fragment)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 PEG 3350, Na-cacodylate, MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.69 α = 90 b = 89.77 β = 90 c = 189.07 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2003-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.9795 APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.3 27.7 98.1 0.064 9.6 6.7 53175 53175
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 94.8 0.262 2.9 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.3 26.44 50430 50430 2687 97.91 0.22046 0.21668 0.231 0.29227 0.303 RANDOM 39.487
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] -0.1 0.17 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.962 r_dihedral_angle_4_deg 21.553 r_dihedral_angle_3_deg 19.386 r_dihedral_angle_1_deg 5.925 r_scangle_it 3.636 r_scbond_it 2.335 r_angle_refined_deg 1.592 r_mcangle_it 1.338 r_mcbond_it 0.946 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.962 r_dihedral_angle_4_deg 21.553 r_dihedral_angle_3_deg 19.386 r_dihedral_angle_1_deg 5.925 r_scangle_it 3.636 r_scbond_it 2.335 r_angle_refined_deg 1.592 r_mcangle_it 1.338 r_mcbond_it 0.946 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.258 r_symmetry_hbond_refined 0.228 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.11 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8410 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 1
Software Software Software Name Purpose MAR345 data collection XDS data reduction SOLVE phasing SHARP phasing REFMAC refinement XDS data scaling