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The crystal structure of D-amino acid amidase from Ochrobactrum anthropi SV3 complexed with D-Phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D83 PDB entry, 2D83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.067 α = 90 b = 123.702 β = 104.44 c = 116.046 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 RIGAKU JUPITER 210 2005-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 99.9 0.11 0.099 80647 80614 1
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) 2.4 2.49 99.6 0.486 0.434
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 (All) 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, 2D83 2.4 19.87 77883 77883 4106 99.56 0.19917 0.19917 0.19548 0.1952 0.26873 0.2667 RANDOM 31.24
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.831 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 6.393 r_scangle_it 1.906 r_angle_refined_deg 1.262 r_scbond_it 1.186 r_mcangle_it 0.871 r_metal_ion_refined 0.561 r_mcbond_it 0.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.831 r_dihedral_angle_4_deg 19.833 r_dihedral_angle_3_deg 16.349 r_dihedral_angle_1_deg 6.393 r_scangle_it 1.906 r_angle_refined_deg 1.262 r_scbond_it 1.186 r_mcangle_it 0.871 r_metal_ion_refined 0.561 r_mcbond_it 0.472 r_nbtor_refined 0.3 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16274 Nucleic Acid Atoms Solvent Atoms 745 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement JUPITOR210 data reduction DENZO data reduction SCALEPACK data scaling MLPHARE phasing