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Crystal structure of ureidoglycine-glyoxylate aminotransferase (pucG) from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVO PDB ENTRY 1JVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 293 30% PEG MME550, 0.1M NaCl, 0.1M Bicine, pH9.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.4 α = 90 b = 95.99 β = 114.23 c = 101.29 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 CCD MAR CCD 165 mm Mirrors 2009-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.2 ELETTRA 5.2R
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 2.05 27.69 97.9 0.056 9.6 3.7 54886 54886
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) 2.05 2.16 85.8 0.409 2.5 3.4 6971
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 (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 1JVO 2.06 27.69 54886 52089 2787 99.51 0.1961 0.19341 0.2103 0.24689 0.26 RANDOM 28.436
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] -1.81 -1.7 2.22 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.265 r_dihedral_angle_4_deg 21.27 r_dihedral_angle_3_deg 17.524 r_dihedral_angle_1_deg 6.964 r_scangle_it 4.731 r_scbond_it 3.219 r_angle_refined_deg 2.052 r_mcangle_it 1.744 r_mcbond_it 1.015 r_chiral_restr 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.265 r_dihedral_angle_4_deg 21.27 r_dihedral_angle_3_deg 17.524 r_dihedral_angle_1_deg 6.964 r_scangle_it 4.731 r_scbond_it 3.219 r_angle_refined_deg 2.052 r_mcangle_it 1.744 r_mcbond_it 1.015 r_chiral_restr 0.196 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6002 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 30
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling