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Mutagenesis of a Rhodobacteraceae L-haloacid dehalogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YML PDB ENTRY 2YML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.25 45.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.87 α = 90 b = 68.95 β = 90 c = 156.8 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 287 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.89 28.55 99.9 0.07 18.4 6.3 259162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.84 8.25 100 0.77 2.2 6.3
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 PDB ENTRY 2YML 1.84 28.55 38929 2061 99.9 0.17511 0.17242 0.1725 0.22735 0.2275 RANDOM 25.205
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] 0.17 -0.34 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.961 r_dihedral_angle_4_deg 16.098 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_1_deg 5.054 r_mcangle_it 4.404 r_scbond_it 4.267 r_mcbond_it 3.206 r_angle_refined_deg 1.33 r_chiral_restr 0.085 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.961 r_dihedral_angle_4_deg 16.098 r_dihedral_angle_3_deg 14.156 r_dihedral_angle_1_deg 5.054 r_mcangle_it 4.404 r_scbond_it 4.267 r_mcbond_it 3.206 r_angle_refined_deg 1.33 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3484 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement