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Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pyrococcus furiosus in complex with hypoxanthine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7R37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 comprising 26% (w/v) PEG 1500 with 100 mM MMT, pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.92 36.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.929 α = 90 b = 111.929 β = 90 c = 121.961 γ = 90
Symmetry Space Group P 42 21 2
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 16M 2021-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.06 48.31 94.8 0.12 0.99 17.7 22.1 45682
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 2.06 2.12 0.61
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 2.064 48.31 45633 2151 94.594 0.167 0.165 0.1748 0.206 0.214 38.425
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] -0.24 -0.24 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.374 r_dihedral_angle_3_deg 13.481 r_dihedral_angle_2_deg 13.465 r_lrange_it 8.101 r_lrange_other 8.1 r_scangle_it 7.004 r_scangle_other 7.003 r_dihedral_angle_1_deg 6.26 r_scbond_it 4.688 r_scbond_other 4.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.374 r_dihedral_angle_3_deg 13.481 r_dihedral_angle_2_deg 13.465 r_lrange_it 8.101 r_lrange_other 8.1 r_scangle_it 7.004 r_scangle_other 7.003 r_dihedral_angle_1_deg 6.26 r_scbond_it 4.688 r_scbond_other 4.688 r_mcangle_it 3.632 r_mcangle_other 3.632 r_mcbond_it 2.699 r_mcbond_other 2.699 r_angle_refined_deg 1.643 r_angle_other_deg 0.546 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.179 r_nbd_other 0.161 r_symmetry_nbd_refined 0.141 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.075 r_ncsr_local_group_1 0.066 r_dihedral_angle_other_2_deg 0.014 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6646 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing