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Crystal structure of Glutamate 1-Semialdehyde Aminotransferase complexed with pyridoxamine-5'-phosphate From Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GSB PDB ENTRY 3GSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 100mM Bicine, 30%(w/v) PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.92 35.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.251 α = 90 b = 55.761 β = 132.02 c = 80.504 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE MARRESEARCH 2006-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
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 2.3 59.761 0.07 15153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.359 1061
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 ENTRY 3GSB 2.3 20 14880 779 97.08 0.19547 0.19342 0.1962 0.23362 0.236 RANDOM 24.336
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] -0.38 -0.99 0.82 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.823 r_dihedral_angle_4_deg 18.192 r_dihedral_angle_3_deg 14.028 r_dihedral_angle_1_deg 4.724 r_scangle_it 1.452 r_angle_refined_deg 1.05 r_scbond_it 0.835 r_mcangle_it 0.561 r_mcbond_it 0.322 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.823 r_dihedral_angle_4_deg 18.192 r_dihedral_angle_3_deg 14.028 r_dihedral_angle_1_deg 4.724 r_scangle_it 1.452 r_angle_refined_deg 1.05 r_scbond_it 0.835 r_mcangle_it 0.561 r_mcbond_it 0.322 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.189 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3270 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection AUTOMAR data reduction MOLREP phasing