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Crystal structure of LooH in complex with I-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 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.201 α = 90 b = 123.744 β = 97.79 c = 82.039 γ = 90
Symmetry Space Group P 1 21 1
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 2021-08-10 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) 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 1.68 30 98.7 0.051 0.033 19.94 3.3 86662
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.74 99.7 0.748 0.638 3.2
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 1.8 27.11 86662 4543 97.52 0.18158 0.17989 0.1884 0.21387 0.22 RANDOM 15.68
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] 0.01 -0.01 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.028 r_dihedral_angle_1_deg 6.414 r_long_range_B_refined 3.405 r_long_range_B_other 3.405 r_scangle_other 2.1 r_dihedral_angle_2_deg 1.892 r_mcangle_it 1.499 r_mcangle_other 1.499 r_scbond_it 1.256 r_scbond_other 1.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.028 r_dihedral_angle_1_deg 6.414 r_long_range_B_refined 3.405 r_long_range_B_other 3.405 r_scangle_other 2.1 r_dihedral_angle_2_deg 1.892 r_mcangle_it 1.499 r_mcangle_other 1.499 r_scbond_it 1.256 r_scbond_other 1.256 r_angle_refined_deg 1.151 r_mcbond_it 0.891 r_mcbond_other 0.891 r_angle_other_deg 0.779 r_chiral_restr 0.177 r_gen_planes_other 0.006 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 8440 Nucleic Acid Atoms Solvent Atoms 749 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement SCALA data scaling HKL-2000 data reduction MOLREP phasing