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HydE from T. maritima in complex with 4R-TCA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CIW
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 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51 α = 90 b = 79.19 β = 90 c = 86.24 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 2013-07-12 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) R Sym I (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 1.18 44 99.6 0.067 12.65 4.5 114847
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.25 98.9 0.779 0.7 1.79 4.3
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 3CIW 1.18 43.9 109463 5384 99.67 0.119 0.11782 0.1176 0.14217 0.1419 RANDOM 17.04
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] 0.74 -0.01 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.299 r_sphericity_free 30.371 r_dihedral_angle_4_deg 18.381 r_dihedral_angle_3_deg 13.401 r_sphericity_bonded 9.334 r_rigid_bond_restr 6.742 r_dihedral_angle_1_deg 6.469 r_scangle_other 3.507 r_long_range_B_refined 3.454 r_long_range_B_other 3.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.299 r_sphericity_free 30.371 r_dihedral_angle_4_deg 18.381 r_dihedral_angle_3_deg 13.401 r_sphericity_bonded 9.334 r_rigid_bond_restr 6.742 r_dihedral_angle_1_deg 6.469 r_scangle_other 3.507 r_long_range_B_refined 3.454 r_long_range_B_other 3.454 r_scbond_it 3.146 r_scbond_other 3.146 r_angle_refined_deg 2.591 r_mcangle_other 2.158 r_mcangle_it 2.157 r_mcbond_it 1.937 r_mcbond_other 1.934 r_angle_other_deg 1.331 r_chiral_restr 0.185 r_bond_refined_d 0.025 r_gen_planes_refined 0.014 r_gen_planes_other 0.005 r_bond_other_d 0.004 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 2757 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 217
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing