☰ Navigation Tabs
Unique Choloylglycine Hydrolase(CGH) member Mutant (C1S) from Shewanella loihica PV-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293.15 PEG 3350, sodium sulphate, 2-Methyl-2, 4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.38 48.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.788 α = 90 b = 52.42 β = 115.96 c = 99.205 γ = 90
Symmetry Space Group C 1 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 FLAT PANEL RAYONIX MX-225 2016-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.97855 ESRF MASSIF-3
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 1.5 50 100 12.2 4.9 105996
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 3HBC 1.5 35.891 105996 5588 99.8 0.18574 0.18458 0.1843 0.20767 0.2075 RANDOM 19.563
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] 0.07 0.14 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.546 r_dihedral_angle_4_deg 16.125 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_1_deg 5.926 r_long_range_B_refined 4.681 r_long_range_B_other 4.681 r_scangle_other 4.306 r_angle_other_deg 3.724 r_scbond_it 2.912 r_scbond_other 2.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.546 r_dihedral_angle_4_deg 16.125 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_1_deg 5.926 r_long_range_B_refined 4.681 r_long_range_B_other 4.681 r_scangle_other 4.306 r_angle_other_deg 3.724 r_scbond_it 2.912 r_scbond_other 2.912 r_mcangle_it 2.127 r_mcangle_other 2.127 r_angle_refined_deg 2.076 r_mcbond_it 1.611 r_mcbond_other 1.605 r_chiral_restr 0.135 r_bond_refined_d 0.022 r_gen_planes_other 0.018 r_gen_planes_refined 0.011 r_bond_other_d 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 5322 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHENIX phasing