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Crystal structure of LooH in complex with FAD
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 8.5 293 0.2 M Sodium formate, 0.1 M BICINE, 20% w/v polyethylene glycol monomethyl ether 5000
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.296 α = 90 b = 101.622 β = 90 c = 125.769 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 2020-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 2.44 30 99.8 0.037 0.04 0.016 44.47 6.4 44717
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 2.44 2.53 99.4 0.082 0.089 0.036 0.994 21.14 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.44 28.39 42398 2245 99.46 0.20885 0.20575 0.2105 0.26714 0.2714 RANDOM 34.922
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] 0.04 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.781 r_dihedral_angle_4_deg 17.273 r_dihedral_angle_3_deg 14.423 r_dihedral_angle_1_deg 6.946 r_long_range_B_other 5.443 r_long_range_B_refined 5.442 r_scangle_other 3.306 r_mcangle_it 3.217 r_mcangle_other 3.217 r_scbond_it 1.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.781 r_dihedral_angle_4_deg 17.273 r_dihedral_angle_3_deg 14.423 r_dihedral_angle_1_deg 6.946 r_long_range_B_other 5.443 r_long_range_B_refined 5.442 r_scangle_other 3.306 r_mcangle_it 3.217 r_mcangle_other 3.217 r_scbond_it 1.955 r_scbond_other 1.954 r_mcbond_it 1.917 r_mcbond_other 1.917 r_angle_refined_deg 1.293 r_angle_other_deg 1.184 r_chiral_restr 0.056 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 8428 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement SCALA data scaling HKL-2000 data reduction MOLREP phasing