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Structural and enzymatic characterization of an esterase from a metagenomic library
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XUA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 Bis-Tris, pH 6.5, 0.1 M NaCl, 1.3 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.65 α = 90 b = 105.95 β = 90 c = 145.94 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 IMAGE PLATE RIGAKU RAXIS IV++ 2014-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.3 30 99.9 0.1 0.04 0.77 13.4 5.7 50655
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.4 2.2 5.9
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 2XUA 2.35 19.87 44300 2268 98.94 0.1949 0.19295 0.1963 0.233 0.236 RANDOM 43.385
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] -0.03 0.05 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.191 r_dihedral_angle_4_deg 19.278 r_dihedral_angle_3_deg 15.867 r_dihedral_angle_1_deg 5.721 r_long_range_B_refined 5.002 r_long_range_B_other 4.972 r_scangle_other 3.287 r_mcangle_it 2.621 r_mcangle_other 2.621 r_scbond_it 1.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.191 r_dihedral_angle_4_deg 19.278 r_dihedral_angle_3_deg 15.867 r_dihedral_angle_1_deg 5.721 r_long_range_B_refined 5.002 r_long_range_B_other 4.972 r_scangle_other 3.287 r_mcangle_it 2.621 r_mcangle_other 2.621 r_scbond_it 1.984 r_scbond_other 1.978 r_mcbond_it 1.604 r_mcbond_other 1.603 r_angle_refined_deg 1.549 r_angle_other_deg 0.983 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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 8189 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement PHASER phasing MOSFLM data reduction SCALA data scaling