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Crystal Structure of DEH Reductase A1-R Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 293 PEG 4000, Lithium chloride, tris (hydroxymethyl) aminomethane
Crystal Properties Matthews coefficient Solvent content 1.99 38.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.5 α = 90 b = 104.5 β = 90 c = 68.116 γ = 120
Symmetry Space Group P 32 2 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 CCD ADSC QUANTUM 315 2014-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 3.11 50 99.5 67.5 11.3 7885
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 3AFM 3.11 50 7336 361 96.36 0.20177 0.19725 0.1954 0.29465 0.2813 RANDOM 78.512
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] 0.31 0.16 0.31 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.5 r_dihedral_angle_3_deg 14.589 r_dihedral_angle_4_deg 12.333 r_long_range_B_refined 7.282 r_long_range_B_other 7.282 r_dihedral_angle_1_deg 6.059 r_mcangle_it 4.91 r_mcangle_other 4.909 r_scangle_other 4.24 r_mcbond_it 3.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.5 r_dihedral_angle_3_deg 14.589 r_dihedral_angle_4_deg 12.333 r_long_range_B_refined 7.282 r_long_range_B_other 7.282 r_dihedral_angle_1_deg 6.059 r_mcangle_it 4.91 r_mcangle_other 4.909 r_scangle_other 4.24 r_mcbond_it 3.004 r_mcbond_other 3.004 r_scbond_it 2.561 r_scbond_other 2.56 r_angle_refined_deg 1.025 r_angle_other_deg 0.7 r_chiral_restr 0.054 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3598 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement