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Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C. Cloacamonas acidaminovorans in complex with the product acetoacetate
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 18% PEG3350, 0.220 M MG FORMATE, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.1 α = 90 b = 102.1 β = 90 c = 100.736 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 1.4 45 99.3 0.07 12.5 7.2 104015 3 17.93
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 1.4 1.48 98.5 0.5 3 6.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Y7D 1.4 28 103836 5254 99.18 0.1676 0.1666 0.1639 0.1863 0.1852 RANDOM 20.91
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] 0.3491 0.3491 -0.6981
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.68 t_other_torsion 2.61 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 4.68 t_other_torsion 2.61 t_angle_deg 1.06 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4223 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 24
Software Software Software Name Purpose BUSTER refinement MOSFLM data reduction SCALA data scaling MOLREP phasing