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Crystal structure of KtzT-C197A in complex with HEME and substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 0.1 M ammonium acetate, 0.1 M Tris pH 8.0,
1.0 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.73 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.688 α = 90 b = 101.088 β = 90 c = 110.977 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 EIGER X 9M 2023-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
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 25 97.6 0.113 0.125 0.054 0.998 7.4 5.4 67091
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 2.01 2.08 96.1 0.577 0.655 0.303 0.895 4.4
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 24.95 63521 3309 96.59 0.24315 0.24008 0.2465 0.30242 0.3084 RANDOM 30.493
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] 1.93 -2.35 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.569 r_dihedral_angle_4_deg 17.572 r_dihedral_angle_3_deg 14.586 r_long_range_B_refined 6.9 r_long_range_B_other 6.9 r_dihedral_angle_1_deg 6.776 r_scangle_other 4.524 r_mcangle_it 3.76 r_mcangle_other 3.76 r_scbond_it 2.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.569 r_dihedral_angle_4_deg 17.572 r_dihedral_angle_3_deg 14.586 r_long_range_B_refined 6.9 r_long_range_B_other 6.9 r_dihedral_angle_1_deg 6.776 r_scangle_other 4.524 r_mcangle_it 3.76 r_mcangle_other 3.76 r_scbond_it 2.909 r_scbond_other 2.909 r_mcbond_it 2.563 r_mcbond_other 2.562 r_angle_refined_deg 1.659 r_angle_other_deg 1.36 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 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 6427 Nucleic Acid Atoms Solvent Atoms 744 Heterogen Atoms 192
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing