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The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with L-phenylalanine amide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DRW DAA native structure (2DRW)
Crystallization Crystal Properties Matthews coefficient Solvent content 2.2 44.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.711 α = 90 b = 123.396 β = 104.36 c = 115.477 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 ADSC QUANTUM 315 2005-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.2 50 98.1 0.072 0.06 4.7 103243
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) 2.2 2.28 85.6 0.265 0.243 3.1
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 DAA native structure (2DRW) 2.2 19.82 97895 5162 98.09 0.19035 0.18689 0.1869 0.25613 0.2555 RANDOM 27.168
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 20.71 r_dihedral_angle_3_deg 15.943 r_dihedral_angle_1_deg 6.59 r_scangle_it 2.615 r_scbond_it 1.68 r_angle_refined_deg 1.356 r_mcangle_it 1.093 r_mcbond_it 0.592 r_metal_ion_refined 0.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 20.71 r_dihedral_angle_3_deg 15.943 r_dihedral_angle_1_deg 6.59 r_scangle_it 2.615 r_scbond_it 1.68 r_angle_refined_deg 1.356 r_mcangle_it 1.093 r_mcbond_it 0.592 r_metal_ion_refined 0.374 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_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 16144 Nucleic Acid Atoms Solvent Atoms 1188 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing