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Alpha-amino epsilon-caprolactam racemase D210A mutant in complex with PLP and geminal diamine intermediate
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 2.01 38.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.21 α = 90 b = 79.111 β = 112.82 c = 58.971 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 2M 2015-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 1.5 45.79 99.2 0.028 26.1 4.1 57829
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 1.5 1.53 0.22
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 1.5 45.79 54969 2859 99.2 0.141 0.14 0.1401 0.168 0.1674 RANDOM 16.59
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] 0.12 0.25 -0.59 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.891 r_dihedral_angle_4_deg 22.658 r_dihedral_angle_3_deg 12.745 r_dihedral_angle_1_deg 6.132 r_long_range_B_refined 5.118 r_long_range_B_other 5.117 r_scangle_other 4.038 r_scbond_it 2.837 r_scbond_other 2.836 r_mcangle_it 2.378
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.891 r_dihedral_angle_4_deg 22.658 r_dihedral_angle_3_deg 12.745 r_dihedral_angle_1_deg 6.132 r_long_range_B_refined 5.118 r_long_range_B_other 5.117 r_scangle_other 4.038 r_scbond_it 2.837 r_scbond_other 2.836 r_mcangle_it 2.378 r_mcangle_other 2.378 r_angle_refined_deg 2.36 r_mcbond_other 1.721 r_mcbond_it 1.72 r_angle_other_deg 1.522 r_chiral_restr 0.202 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 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 3196 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing