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Crystal structure of LooH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M HEPES, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.294 α = 90 b = 130.493 β = 90 c = 168.474 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 PIXEL DECTRIS EIGER2 X 9M 2021-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 1.63 30 99.9 0.052 0.057 0.023 30.33 6 143017
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.7 99.9 0.517 0.571 0.241 0.861 2.88 5.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.63 26.2 133353 7148 97.95 0.19398 0.19244 0.201 0.22285 0.2287 RANDOM 14.044
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.33 r_dihedral_angle_1_deg 6.291 r_long_range_B_refined 3.449 r_long_range_B_other 3.211 r_dihedral_angle_2_deg 1.782 r_scangle_other 1.637 r_mcangle_it 1.387 r_mcangle_other 1.387 r_angle_refined_deg 1.12 r_scbond_it 0.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.33 r_dihedral_angle_1_deg 6.291 r_long_range_B_refined 3.449 r_long_range_B_other 3.211 r_dihedral_angle_2_deg 1.782 r_scangle_other 1.637 r_mcangle_it 1.387 r_mcangle_other 1.387 r_angle_refined_deg 1.12 r_scbond_it 0.967 r_scbond_other 0.967 r_mcbond_it 0.796 r_mcbond_other 0.796 r_angle_other_deg 0.47 r_chiral_restr 0.063 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 8435 Nucleic Acid Atoms Solvent Atoms 945 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALA data scaling HKL-2000 data reduction MOLREP phasing