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Unique Choloylglycine Hydrolase(CGH) member 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 2.33 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.397 α = 90 b = 52.337 β = 103.81 c = 140.068 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS PILATUS3 2M 2015-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.972400 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 89.43 97.6 0.06 0.997 13.8 3.5 109332
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 89.43 103814 5491 97.53 0.19135 0.19004 0.1997 0.21616 0.2253 RANDOM 14.372
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.073 r_dihedral_angle_4_deg 14.881 r_dihedral_angle_3_deg 12.852 r_dihedral_angle_1_deg 6.176 r_long_range_B_other 4.42 r_long_range_B_refined 4.419 r_scangle_other 3.902 r_scbond_it 2.739 r_scbond_other 2.738 r_angle_refined_deg 2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.073 r_dihedral_angle_4_deg 14.881 r_dihedral_angle_3_deg 12.852 r_dihedral_angle_1_deg 6.176 r_long_range_B_other 4.42 r_long_range_B_refined 4.419 r_scangle_other 3.902 r_scbond_it 2.739 r_scbond_other 2.738 r_angle_refined_deg 2.24 r_mcangle_other 1.973 r_mcangle_it 1.972 r_mcbond_it 1.439 r_mcbond_other 1.427 r_angle_other_deg 1.146 r_chiral_restr 0.152 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 172 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHENIX phasing PHENIX model building