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Crystal structure of LooH in complex with Trp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 300 0.1 M HEPES, 25% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.362 α = 90 b = 96.771 β = 90 c = 123.837 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 ADSC QUANTUM 210 2021-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
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 2.15 30 98.4 0.046 0.051 0.021 33.066 5.6 61009
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 2.15 2.23 98.5 0.639 0.701 0.281 0.868 2.577 5.8
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 2.15 28.28 61009 2832 98.28 0.20206 0.19942 0.25701 0.2663 RANDOM 47.514
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 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.596 r_long_range_B_refined 6.953 r_long_range_B_other 6.952 r_dihedral_angle_1_deg 6.413 r_dihedral_angle_2_deg 5.948 r_scangle_other 5.539 r_mcangle_it 4.079 r_mcangle_other 4.078 r_scbond_it 3.517 r_scbond_other 3.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.596 r_long_range_B_refined 6.953 r_long_range_B_other 6.952 r_dihedral_angle_1_deg 6.413 r_dihedral_angle_2_deg 5.948 r_scangle_other 5.539 r_mcangle_it 4.079 r_mcangle_other 4.078 r_scbond_it 3.517 r_scbond_other 3.517 r_mcbond_it 2.814 r_mcbond_other 2.814 r_angle_refined_deg 1.168 r_angle_other_deg 0.664 r_chiral_restr 0.066 r_gen_planes_other 0.007 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 132 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement SCALA data scaling HKL-2000 data reduction MOLREP phasing