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Crystal structure of D-phenylglycine aminotransferase (D-PhgAT) from Pseudomonas strutzeri ST-201
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.42 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.684 α = 90 b = 74.684 β = 90 c = 147.411 γ = 120
Symmetry Space Group P 31 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 100 CCD ADSC QUANTUM 2004-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.00000 SPring-8 BL44B2
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 2.3 50 19737
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 MOLECULAR REPLACEMENT THROUGHOUT 2.3 31.6 19737 1073 95.38 0.18552 0.18351 0.1914 0.22317 0.2284 RANDOM 38.128
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] 0.2 0.1 0.2 -0.31
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.934 r_dihedral_angle_1_deg 6.403 r_scbond_it 4.35 r_mcangle_it 3.149 r_angle_refined_deg 2.527 r_mcbond_it 1.796 r_angle_other_deg 1.143 r_nbd_other 0.26 r_symmetry_vdw_other 0.255 r_nbd_refined 0.253
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.934 r_dihedral_angle_1_deg 6.403 r_scbond_it 4.35 r_mcangle_it 3.149 r_angle_refined_deg 2.527 r_mcbond_it 1.796 r_angle_other_deg 1.143 r_nbd_other 0.26 r_symmetry_vdw_other 0.255 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.187 r_symmetry_hbond_refined 0.182 r_symmetry_vdw_refined 0.155 r_nbtor_other 0.106 r_bond_refined_d 0.037 r_gen_planes_refined 0.015 r_gen_planes_other 0.014 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 3055 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing