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HydE from T. maritima in complex with (2R,4R)-MeSeTDA, 5'-deoxyadenosine and methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG4000, Lithium sulfate, CHAPS, TrisHCl
Crystal Properties Matthews coefficient Solvent content 2.11 41.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.8 α = 90 b = 78.87 β = 90 c = 86.25 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.979 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.35 44 99.8 15.27 5.9 76623
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.43 0.939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3IIX 1.35 38.27 72790 3833 99.87 0.11982 0.11904 0.1185 0.13519 0.131 RANDOM 17.191
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] 1.29 -0.13 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.425 r_sphericity_free 32.399 r_dihedral_angle_4_deg 16.393 r_dihedral_angle_3_deg 11.887 r_sphericity_bonded 9.392 r_rigid_bond_restr 9.214 r_dihedral_angle_1_deg 5.946 r_long_range_B_refined 3.758 r_long_range_B_other 3.758 r_scangle_other 3.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.425 r_sphericity_free 32.399 r_dihedral_angle_4_deg 16.393 r_dihedral_angle_3_deg 11.887 r_sphericity_bonded 9.392 r_rigid_bond_restr 9.214 r_dihedral_angle_1_deg 5.946 r_long_range_B_refined 3.758 r_long_range_B_other 3.758 r_scangle_other 3.494 r_scbond_it 3.135 r_scbond_other 3.135 r_angle_refined_deg 2.277 r_mcangle_it 1.811 r_mcangle_other 1.811 r_mcbond_it 1.673 r_mcbond_other 1.673 r_angle_other_deg 1.434 r_chiral_restr 0.227 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2741 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 215
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing