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The crystal structure of Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase from Burkholderia cenocepacia J2315
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FR8 PDB ENTRY 4FR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 Morpheus Screen well E2:
0.12 Ethylene glycols, 0.1M buffer 1, 30% ethylene glycol/PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.33 47.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.31 α = 91.7 b = 104.19 β = 99.04 c = 108.28 γ = 90.02
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 MAR scanner 300 mm plate 2013-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97919 APS 21-ID-D
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 1.85 50 97.8 0.107 13.3 5.8 332765 325553 11.1
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 1.85 1.9 96.6 0.548 3.52 5.9 23867
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 4FR8 1.85 48.19 309137 16432 97.85 0.19097 0.1888 0.1977 0.23175 0.2369 RANDOM 16.189
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] -0.84 0.05 0.05 -0.02 -0.3 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.42 r_dihedral_angle_4_deg 17.588 r_dihedral_angle_3_deg 12.444 r_dihedral_angle_1_deg 6.402 r_long_range_B_refined 4.309 r_long_range_B_other 4.309 r_angle_refined_deg 1.513 r_scangle_other 1.253 r_mcangle_it 0.893 r_mcangle_other 0.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.42 r_dihedral_angle_4_deg 17.588 r_dihedral_angle_3_deg 12.444 r_dihedral_angle_1_deg 6.402 r_long_range_B_refined 4.309 r_long_range_B_other 4.309 r_angle_refined_deg 1.513 r_scangle_other 1.253 r_mcangle_it 0.893 r_mcangle_other 0.893 r_angle_other_deg 0.815 r_scbond_it 0.792 r_scbond_other 0.791 r_mcbond_it 0.541 r_mcbond_other 0.541 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29322 Nucleic Acid Atoms Solvent Atoms 3341 Heterogen Atoms 124
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling