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Crystal structure of HAT1 in complex with XS380871
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P0W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 25% w/v lithium sulfate, 0.2 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.889 α = 84.376 b = 87.838 β = 80.069 c = 118.029 γ = 76.763
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 PILATUS3 X 6M 2024-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97741 ALS 5.0.2
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 2.58 50 96 0.127 0.155 0.088 0.984 5.7 2.8 92226
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 2.58 2.62 76.5 0.653 0.825 0.495 0.602 2.3
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 (All) 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 2.58 49.454 91788 4581 96.101 0.237 0.2349 0.2361 0.2702 0.2707 RANDOM 44.342
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] -0.582 -1.128 0.033 -0.064 1.341 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.879 r_dihedral_angle_3_deg 13.194 r_dihedral_angle_2_deg 8.3 r_dihedral_angle_1_deg 6.835 r_lrange_it 3.082 r_lrange_other 3.082 r_scangle_it 1.852 r_scangle_other 1.852 r_mcangle_it 1.811 r_mcangle_other 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.879 r_dihedral_angle_3_deg 13.194 r_dihedral_angle_2_deg 8.3 r_dihedral_angle_1_deg 6.835 r_lrange_it 3.082 r_lrange_other 3.082 r_scangle_it 1.852 r_scangle_other 1.852 r_mcangle_it 1.811 r_mcangle_other 1.81 r_angle_refined_deg 1.266 r_scbond_it 1.098 r_scbond_other 1.098 r_mcbond_it 1.063 r_mcbond_other 1.063 r_angle_other_deg 0.438 r_symmetry_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.213 r_nbd_refined 0.205 r_nbd_other 0.202 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.164 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_12 0.067 r_ncsr_local_group_6 0.066 r_ncsr_local_group_15 0.065 r_ncsr_local_group_13 0.064 r_ncsr_local_group_14 0.062 r_ncsr_local_group_2 0.061 r_ncsr_local_group_25 0.061 r_chiral_restr 0.06 r_ncsr_local_group_7 0.06 r_ncsr_local_group_8 0.06 r_ncsr_local_group_24 0.06 r_ncsr_local_group_16 0.059 r_ncsr_local_group_21 0.059 r_ncsr_local_group_20 0.057 r_ncsr_local_group_5 0.056 r_ncsr_local_group_11 0.056 r_ncsr_local_group_18 0.056 r_ncsr_local_group_1 0.054 r_ncsr_local_group_17 0.054 r_ncsr_local_group_22 0.054 r_ncsr_local_group_23 0.054 r_ncsr_local_group_26 0.054 r_ncsr_local_group_4 0.053 r_ncsr_local_group_27 0.053 r_ncsr_local_group_9 0.049 r_ncsr_local_group_28 0.047 r_ncsr_local_group_10 0.046 r_ncsr_local_group_19 0.046 r_symmetry_xyhbond_nbd_other 0.041 r_ncsr_local_group_3 0.039 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20079 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 256
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction