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Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from Candidatus Cloacamonas acidaminovorans (tetragonal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y7D PDB ENTRY 2Y7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20% PEG3350, 0.220 M MG FORMATE, 26.4% GLYCEROL, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.13 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.188 α = 90 b = 102.188 β = 90 c = 101.07 γ = 90
Symmetry Space Group P 43 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 110 CCD ADSC CCD KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS 2010-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 1.28 50 97.6 0.08 12.4 7 133532 3
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 1.28 1.35 89.6 0.47 3.3 5.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Y7D 1.28 45.76 126786 6691 97.3 0.14465 0.14333 0.1702 0.1942 RANDOM 15.113
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] -0.11 -0.11 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.855 r_dihedral_angle_4_deg 17.188 r_dihedral_angle_3_deg 11.964 r_sphericity_bonded 10.789 r_sphericity_free 7.631 r_dihedral_angle_1_deg 5.995 r_rigid_bond_restr 3.487 r_angle_refined_deg 1.467 r_angle_other_deg 0.938 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.855 r_dihedral_angle_4_deg 17.188 r_dihedral_angle_3_deg 11.964 r_sphericity_bonded 10.789 r_sphericity_free 7.631 r_dihedral_angle_1_deg 5.995 r_rigid_bond_restr 3.487 r_angle_refined_deg 1.467 r_angle_other_deg 0.938 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4223 Nucleic Acid Atoms Solvent Atoms 585 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing