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Crystal structure of HpeI from Rhodococcus rhodochrous GD02
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, SITTING DROP 293 25% PEG 1500,
0.1 M PCTP (Sodium propionate, Sodium cacodylate trihydrate, Bis-Tris propane) pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.06 40.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.902 α = 90 b = 57.27 β = 99.591 c = 67.118 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 EIGER2 XE 16M 2023-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.803 66.18 90.7 0.164 0.067 0.996 6.9 7 14742
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.803 1.972 66 1.312 0.528 0.642 1.4 7.2
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 1.803 66.18 14742 715 46.353 0.21 0.2072 0.2074 0.2552 0.2546 24.712
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] -0.256 0.07 -0.057 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.841 r_dihedral_angle_6_deg 14.655 r_dihedral_angle_1_deg 7.501 r_dihedral_angle_2_deg 6.976 r_lrange_it 6.022 r_scangle_it 3.656 r_mcangle_it 2.751 r_scbond_it 2.317 r_angle_refined_deg 1.778 r_mcbond_it 1.686
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.841 r_dihedral_angle_6_deg 14.655 r_dihedral_angle_1_deg 7.501 r_dihedral_angle_2_deg 6.976 r_lrange_it 6.022 r_scangle_it 3.656 r_mcangle_it 2.751 r_scbond_it 2.317 r_angle_refined_deg 1.778 r_mcbond_it 1.686 r_nbtor_refined 0.304 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.125 r_symmetry_xyhbond_nbd_refined 0.12 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2541 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing