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Crystal structure of AlinE4, a SGNH-hydrolase family esterase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JGG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291.15 1M Sodium acetate, 100mM HEPES, pH 7.5, 50mM Cadmium sulfate
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.783 α = 90 b = 79.783 β = 90 c = 61.01 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315r 2017-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97931 SSRF BL17U1
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 1.18 48.46 99.05 0.073 20 2 64489
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 1.18 1.22 0.645
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4JGG 1.18 48.46 61212 3291 99.043 0.128 0.127 0.1269 0.1546 0.1544 14.738
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] -0.063 -0.063 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.725 r_dihedral_angle_4_deg 22.583 r_dihedral_angle_3_deg 13.932 r_dihedral_angle_1_deg 5.662 r_rigid_bond_restr 5.193 r_scangle_it 3.983 r_scangle_other 3.982 r_scbond_it 3.46 r_scbond_other 3.458 r_lrange_it 3.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.725 r_dihedral_angle_4_deg 22.583 r_dihedral_angle_3_deg 13.932 r_dihedral_angle_1_deg 5.662 r_rigid_bond_restr 5.193 r_scangle_it 3.983 r_scangle_other 3.982 r_scbond_it 3.46 r_scbond_other 3.458 r_lrange_it 3.272 r_lrange_other 3.15 r_angle_refined_deg 2.131 r_mcangle_other 1.862 r_mcangle_it 1.849 r_angle_other_deg 1.662 r_mcbond_it 1.54 r_mcbond_other 1.454 r_symmetry_nbd_refined 0.317 r_nbd_refined 0.272 r_xyhbond_nbd_refined 0.208 r_symmetry_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.2 r_nbd_other 0.188 r_nbtor_refined 0.178 r_chiral_restr 0.139 r_symmetry_nbtor_other 0.091 r_metal_ion_refined 0.073 r_bond_refined_d 0.019 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1439 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PHENIX phasing