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crystal structure of a hairpin exchange variant (LTx) of the targeting LINE-1 retrotransposon endonuclease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VYB PDB ENTRY 1VYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7
Crystal Properties Matthews coefficient Solvent content 2.26 45.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.726 α = 90 b = 70.142 β = 90 c = 130.221 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 287 CCD ADSC CCD 2000-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 20 99.8 0.11 8.8 3 22873 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 100 0.488 2.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VYB 2.3 19.53 21588 1156 99.2 0.217 0.214 0.272 0.3015 RANDOM 29.81
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] 0.02 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.08 r_dihedral_angle_3_deg 19.624 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_1_deg 11.174 r_scangle_it 3.202 r_scbond_it 2.187 r_angle_refined_deg 1.837 r_mcangle_it 1.665 r_mcbond_it 1.478 r_angle_other_deg 1.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.08 r_dihedral_angle_3_deg 19.624 r_dihedral_angle_4_deg 18.815 r_dihedral_angle_1_deg 11.174 r_scangle_it 3.202 r_scbond_it 2.187 r_angle_refined_deg 1.837 r_mcangle_it 1.665 r_mcbond_it 1.478 r_angle_other_deg 1.135 r_symmetry_vdw_other 0.295 r_symmetry_hbond_refined 0.288 r_symmetry_vdw_refined 0.265 r_xyhbond_nbd_refined 0.233 r_nbd_refined 0.221 r_nbd_other 0.212 r_nbtor_refined 0.171 r_chiral_restr 0.113 r_nbtor_other 0.093 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3759 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing