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Crystal structure of HHD2 domain of hRTEL1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9NZ71-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M CHES pH 9.5, 30% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.13 42.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.59 α = 90 b = 60.68 β = 96.13 c = 79.53 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 PIXEL DECTRIS PILATUS 6M 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 50 97.9 0.997 10.53 6 27255
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.44 96.2 0.836 1.99
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 48.14 27249 1363 97.849 0.216 0.2142 0.2182 0.257 0.2539 47.233
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] 1.476 1.373 -0.901 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.234 r_dihedral_angle_3_deg 15.476 r_dihedral_angle_2_deg 9.701 r_lrange_it 6.576 r_lrange_other 6.576 r_dihedral_angle_1_deg 5.116 r_scangle_it 4.176 r_scangle_other 4.175 r_mcangle_it 3.402 r_mcangle_other 3.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.234 r_dihedral_angle_3_deg 15.476 r_dihedral_angle_2_deg 9.701 r_lrange_it 6.576 r_lrange_other 6.576 r_dihedral_angle_1_deg 5.116 r_scangle_it 4.176 r_scangle_other 4.175 r_mcangle_it 3.402 r_mcangle_other 3.402 r_scbond_it 2.669 r_scbond_other 2.669 r_mcbond_it 2.235 r_mcbond_other 2.232 r_angle_refined_deg 1.887 r_angle_other_deg 0.624 r_symmetry_xyhbond_nbd_refined 0.266 r_nbd_refined 0.249 r_nbd_other 0.199 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.175 r_xyhbond_nbd_refined 0.129 r_ncsr_local_group_9 0.113 r_ncsr_local_group_18 0.112 r_ncsr_local_group_16 0.11 r_ncsr_local_group_7 0.109 r_ncsr_local_group_12 0.107 r_ncsr_local_group_1 0.104 r_ncsr_local_group_20 0.104 r_ncsr_local_group_3 0.103 r_ncsr_local_group_19 0.103 r_ncsr_local_group_4 0.1 r_ncsr_local_group_11 0.099 r_ncsr_local_group_13 0.098 r_ncsr_local_group_2 0.096 r_ncsr_local_group_10 0.095 r_ncsr_local_group_17 0.095 r_ncsr_local_group_5 0.092 r_chiral_restr 0.087 r_ncsr_local_group_8 0.082 r_ncsr_local_group_15 0.082 r_ncsr_local_group_6 0.08 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_21 0.073 r_ncsr_local_group_14 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4188 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing