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Crystal structure of KtzT-C197A in complex with HEME
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 2.75 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.817 α = 90 b = 101.256 β = 90 c = 111.066 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 2023-07-01 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 1.81 25 98.5 0.073 0.083 0.039 0.998 9.5 4.2 91871
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 1.81 1.87 95.7 0.419 0.495 0.258 0.93 3.4
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 1.81 24.69 87035 4588 97.47 0.21548 0.21346 0.221 0.25272 0.2595 RANDOM 22.423
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] 1.48 -2.05 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.721 r_dihedral_angle_4_deg 17.903 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 6.498 r_long_range_B_refined 6.253 r_long_range_B_other 6.024 r_scangle_other 4.158 r_mcangle_it 3.128 r_mcangle_other 3.128 r_scbond_it 2.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.721 r_dihedral_angle_4_deg 17.903 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 6.498 r_long_range_B_refined 6.253 r_long_range_B_other 6.024 r_scangle_other 4.158 r_mcangle_it 3.128 r_mcangle_other 3.128 r_scbond_it 2.711 r_scbond_other 2.711 r_mcbond_it 2.141 r_mcbond_other 2.141 r_angle_refined_deg 1.787 r_angle_other_deg 1.427 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 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 6432 Nucleic Acid Atoms Solvent Atoms 1006 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing