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Alpha-amino epsilon-caprolactam racemase in complex with PLP and D/L alpha amino epsilon-caprolactam (internal 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 1.98 37.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.696 α = 90 b = 77.679 β = 112.68 c = 57.602 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 2015-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 1.51 45.03 99.6 0.025 33.9 4.1 55609
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 1.51 1.54 0.057 2734
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 1.51 56.04 52841 2767 99.57 0.1629 0.1612 0.1736 0.19508 0.2047 RANDOM 15.805
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 -0.18 0.49 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.489 r_dihedral_angle_4_deg 22.889 r_dihedral_angle_3_deg 12.611 r_dihedral_angle_1_deg 6.284 r_long_range_B_refined 4.845 r_long_range_B_other 4.844 r_scangle_other 3.754 r_scbond_it 2.62 r_scbond_other 2.619 r_angle_refined_deg 2.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.489 r_dihedral_angle_4_deg 22.889 r_dihedral_angle_3_deg 12.611 r_dihedral_angle_1_deg 6.284 r_long_range_B_refined 4.845 r_long_range_B_other 4.844 r_scangle_other 3.754 r_scbond_it 2.62 r_scbond_other 2.619 r_angle_refined_deg 2.538 r_mcangle_it 2.519 r_mcangle_other 2.518 r_mcbond_it 1.902 r_mcbond_other 1.902 r_angle_other_deg 1.322 r_chiral_restr 0.161 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_gen_planes_other 0.006 r_bond_other_d 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 3074 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing