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The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFT PDB ENTRY 1SFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 293 30% PEG4000, 0.2M magnesium chloride, 0.1M Tris/HCl(pH8.7), 2.9% Sucrose, 42microM PLP, 20mM epsilon-caprolactam, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.85 33.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.581 α = 90 b = 60.653 β = 103.07 c = 105.315 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD Bruker DIP-6040 2007-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 50 98.8 0.088 0.073 4.8 26897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 98.6 0.359 0.32 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1SFT 2.41 40.29 26897 25532 1348 98.6 0.19434 0.19126 0.191 0.25232 0.2488 RANDOM 42.22
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_3_deg 19.241 r_dihedral_angle_1_deg 5.703 r_scangle_it 2.637 r_scbond_it 1.569 r_angle_refined_deg 1.361 r_mcangle_it 1.09 r_mcbond_it 0.609 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.379 r_dihedral_angle_4_deg 21.863 r_dihedral_angle_3_deg 19.241 r_dihedral_angle_1_deg 5.703 r_scangle_it 2.637 r_scbond_it 1.569 r_angle_refined_deg 1.361 r_mcangle_it 1.09 r_mcbond_it 0.609 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6272 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing