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Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxal
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 Pyridoxal, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.22 44.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.732 α = 90 b = 68.732 β = 90 c = 311.5 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 2005-12-11 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 1.6 50 99.9 0.084 9.9 7.4 100019 -3 13.27
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 1.6 1.66 99.9 0.386 7.4 9737
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 1.7 14.84 79313 4123 99.97 0.15543 0.15411 0.18051 0.17 RANDOM 12.8
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 2.789 r_scbond_it 1.809 r_angle_refined_deg 1.243 r_mcangle_it 0.926 r_mcbond_it 0.573 r_nbtor_refined 0.308 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.126
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 2.789 r_scbond_it 1.809 r_angle_refined_deg 1.243 r_mcangle_it 0.926 r_mcbond_it 0.573 r_nbtor_refined 0.308 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.178 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.126 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 778 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling