☰ Navigation Tabs
Crystal structure of Nep1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii OT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9JGB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dihydrate pH 5.6, 2.0 ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.24 α = 90 b = 113.24 β = 90 c = 102.82 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2023-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 70.97 100 0.136 0.141 0.04 0.995 13.3 12.3 13053
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) Redundancy Number Unique Reflections (All) 1 2.2 2.27 100 0.552 0.576 0.164 0.952 12.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 70.97 12283 669 99.2 0.1886 0.18537 0.24986 0.2497 RANDOM 41.882
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] -1.32 -0.66 -1.32 4.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.253 r_dihedral_angle_2_deg 9.936 r_long_range_B_other 9.021 r_long_range_B_refined 9.016 r_dihedral_angle_1_deg 6.91 r_scangle_other 6.029 r_mcangle_it 4.016 r_mcangle_other 4.016 r_scbond_it 3.768 r_scbond_other 3.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.253 r_dihedral_angle_2_deg 9.936 r_long_range_B_other 9.021 r_long_range_B_refined 9.016 r_dihedral_angle_1_deg 6.91 r_scangle_other 6.029 r_mcangle_it 4.016 r_mcangle_other 4.016 r_scbond_it 3.768 r_scbond_other 3.767 r_mcbond_it 2.596 r_mcbond_other 2.59 r_angle_refined_deg 1.532 r_angle_other_deg 0.524 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1871 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 41
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction