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Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxyl-L-alanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z9U PDB ID 2Z9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.05 277 0.1M HEPES, 2M Ammonium sulfate, 5mM Pyridoxyl-L-alanine, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.72 α = 90 b = 68.72 β = 90 c = 311.942 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS V 2006-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.94 50 98.6 0.071 56030 -3
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) 1 1.94 2.01 97 0.27 9.7 5397
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ID 2Z9U 1.94 14.92 52891 2827 98.52 0.14657 0.14457 0.1837 0.1714 RANDOM 18.258
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_scangle_it 3.06 r_scbond_it 1.982 r_angle_refined_deg 1.342 r_mcangle_it 1.039 r_mcbond_it 0.687 r_nbtor_refined 0.304 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.143
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.06 r_scbond_it 1.982 r_angle_refined_deg 1.342 r_mcangle_it 1.039 r_mcbond_it 0.687 r_nbtor_refined 0.304 r_nbd_refined 0.197 r_symmetry_vdw_refined 0.18 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_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 5832 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling