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Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxamine
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, 10mM Pyridoxamine, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.21 44.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.628 α = 90 b = 68.628 β = 90 c = 312.191 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 2005-10-27 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 1.7 50 98.4 0.039 24.4 5.8 82435 -3 14.99
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 1.7 1.76 91.9 0.113 3 7561
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 PDB ID 2Z9U 1.7 14.94 78010 4094 98.44 0.15714 0.15559 0.1563 0.18636 0.1871 RANDOM 14.852
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 2.772 r_scbond_it 1.758 r_angle_refined_deg 1.248 r_mcangle_it 0.89 r_mcbond_it 0.56 r_symmetry_hbond_refined 0.43 r_nbtor_refined 0.308 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.116
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.772 r_scbond_it 1.758 r_angle_refined_deg 1.248 r_mcangle_it 0.89 r_mcbond_it 0.56 r_symmetry_hbond_refined 0.43 r_nbtor_refined 0.308 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.155 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5832 Nucleic Acid Atoms Solvent Atoms 753 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling