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M291I variant of the [FeFe]-hydrogenase maturase HydE from Thermotoga maritima
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in-house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 4000, Thirs ph 8, LiSO4
Crystal Properties Matthews coefficient Solvent content 2.25 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.81 α = 90 b = 82.14 β = 90 c = 70.24 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M 2023-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
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 1.2 51 98.8 0.998 12.96 3.3 115093
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 1.2 1.23 0.465
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 1.2 50.39 109424 5681 99.51 0.12731 0.12601 0.1261 0.15198 0.1522 RANDOM 18.182
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] -0.57 0.82 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.947 r_dihedral_angle_2_deg 6.925 r_dihedral_angle_1_deg 6.085 r_long_range_B_refined 4.902 r_rigid_bond_restr 4.44 r_long_range_B_other 3.737 r_scangle_other 2.155 r_angle_refined_deg 1.884 r_scbond_it 1.828 r_scbond_other 1.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.947 r_dihedral_angle_2_deg 6.925 r_dihedral_angle_1_deg 6.085 r_long_range_B_refined 4.902 r_rigid_bond_restr 4.44 r_long_range_B_other 3.737 r_scangle_other 2.155 r_angle_refined_deg 1.884 r_scbond_it 1.828 r_scbond_other 1.704 r_mcangle_it 1.372 r_mcangle_other 1.371 r_mcbond_it 1.042 r_mcbond_other 1.04 r_angle_other_deg 0.984 r_chiral_restr 0.139 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2849 Nucleic Acid Atoms Solvent Atoms 542 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHENIX phasing