☰ Navigation Tabs
Structure of the glutaminase subunit Pdx2 (YaaE) of PLP synthase from Bacillus subtilis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9G PDB ENTRY 1R9G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 12.4% PEG 8000, 6% ethylene glycol, 100mM cacodylic acid, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.44 α = 90 b = 81.606 β = 90 c = 117.285 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 4 ESRF 2005-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9340 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.73 50 98.4 0.065 17.3 5.3 46456 45697 28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.75 99.9 0.492 2 3.9
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 1R9G 1.73 50 43316 2310 98.37 0.18147 0.17956 0.1889 0.21579 0.2271 RANDOM 29.489
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 1.19 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.867 r_dihedral_angle_4_deg 19.338 r_dihedral_angle_3_deg 14.578 r_dihedral_angle_1_deg 5.761 r_scangle_it 4.556 r_scbond_it 3.017 r_mcangle_it 2.093 r_angle_other_deg 2.007 r_mcbond_it 1.712 r_angle_refined_deg 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.867 r_dihedral_angle_4_deg 19.338 r_dihedral_angle_3_deg 14.578 r_dihedral_angle_1_deg 5.761 r_scangle_it 4.556 r_scbond_it 3.017 r_mcangle_it 2.093 r_angle_other_deg 2.007 r_mcbond_it 1.712 r_angle_refined_deg 1.706 r_symmetry_vdw_other 0.363 r_symmetry_vdw_refined 0.36 r_xyhbond_nbd_refined 0.296 r_nbd_refined 0.249 r_nbd_other 0.239 r_mcbond_other 0.188 r_symmetry_hbond_refined 0.183 r_nbtor_refined 0.181 r_chiral_restr 0.108 r_nbtor_other 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2892 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing