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Crystal structure of Aedes aegypti alanine glyoxylate aminotransferase in complex with glyoxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HUF PDB ENTRY 2HUF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 12% PEG 8000, 0.13 M magnesium acetate, 4% butanol, 0.1 M cacodylic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.082 α = 90 b = 137.082 β = 90 c = 120.425 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 315 mirrors 2006-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25
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 1.75 30 97 0.103 6.8 10.3 82608
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) 1.75 1.81 72.1 0.569 3.3 6174
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 ENTRY 2HUF 1.75 29.18 84634 82584 4106 97.58 0.176 0.176 0.175 0.1738 0.206 0.2053 RANDOM 15.748
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 34.804 r_dihedral_angle_4_deg 19.012 r_dihedral_angle_3_deg 18.13 r_dihedral_angle_1_deg 5.973 r_scangle_it 3.212 r_scbond_it 2.107 r_angle_refined_deg 1.695 r_mcangle_it 1.222 r_mcbond_it 0.754 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.804 r_dihedral_angle_4_deg 19.012 r_dihedral_angle_3_deg 18.13 r_dihedral_angle_1_deg 5.973 r_scangle_it 3.212 r_scbond_it 2.107 r_angle_refined_deg 1.695 r_mcangle_it 1.222 r_mcbond_it 0.754 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.218 r_chiral_restr 0.19 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5956 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction