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Alpha-amino epsilon-caprolactam racemase K241A mutant in complex with D-ACL (external aldimine)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 290 0.2 M MgCl2, 25 % PEG 3350, 0.1 mM HEPES (pH 7.0).
Crystal Properties Matthews coefficient Solvent content 1.95 36.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.1 α = 90 b = 77.49 β = 113.66 c = 58.52 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 120 PIXEL DECTRIS PILATUS 6M-F 2016-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.86 55.27 99.3 0.22 1.3 4 29415
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 1.86 1.91 0.88 2171
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 2ZUK 1.93 55.27 25058 1281 99.25 0.19597 0.19325 0.2014 0.25066 0.2521 RANDOM 14.423
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] 0.04 -0.21 -1.5 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.985 r_dihedral_angle_4_deg 19.411 r_dihedral_angle_3_deg 15.142 r_dihedral_angle_1_deg 6.844 r_long_range_B_refined 3.306 r_long_range_B_other 3.306 r_scangle_other 2.076 r_angle_refined_deg 2.014 r_mcangle_it 1.391 r_mcangle_other 1.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.985 r_dihedral_angle_4_deg 19.411 r_dihedral_angle_3_deg 15.142 r_dihedral_angle_1_deg 6.844 r_long_range_B_refined 3.306 r_long_range_B_other 3.306 r_scangle_other 2.076 r_angle_refined_deg 2.014 r_mcangle_it 1.391 r_mcangle_other 1.391 r_scbond_it 1.373 r_scbond_other 1.373 r_angle_other_deg 1.157 r_mcbond_it 0.924 r_mcbond_other 0.924 r_chiral_restr 0.127 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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 3201 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing