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The crystal structutre of D-amino acid amidase from Ochrobactrum anthropi SV3
Crystallization Crystal Properties Matthews coefficient Solvent content 2.21 44.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.205 α = 90 b = 123.219 β = 104.36 c = 115.706 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 2005-05-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9791, 0.9793, 0.9900 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 47.57 99.2 117625 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 91.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.1 47.57 115879 6124 99.92 0.18526 0.18217 0.183 0.24321 0.2446 RANDOM 26.864
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 34.395 r_dihedral_angle_4_deg 18.841 r_dihedral_angle_3_deg 15.02 r_dihedral_angle_1_deg 6.398 r_scangle_it 2.428 r_scbond_it 1.571 r_angle_refined_deg 1.265 r_mcangle_it 1.054 r_mcbond_it 0.574 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.395 r_dihedral_angle_4_deg 18.841 r_dihedral_angle_3_deg 15.02 r_dihedral_angle_1_deg 6.398 r_scangle_it 2.428 r_scbond_it 1.571 r_angle_refined_deg 1.265 r_mcangle_it 1.054 r_mcbond_it 0.574 r_nbtor_refined 0.302 r_metal_ion_refined 0.248 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.191 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.086 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_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 16380 Nucleic Acid Atoms Solvent Atoms 2056 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement JUPITOR210 data reduction HKL-2000 data scaling SHELXD phasing