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Glutaminase subunit of the plasmodial PLP synthase (Vitamin B6 biosynthesis)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9G 1R9G CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 30% PEG200, 5% PEG8000 buffered with 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.042 α = 90 b = 67.917 β = 92.31 c = 70.327 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 ADSC QUANTUM 210 2004-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9791 ESRF ID29
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 1.62 25 99.9 0.064 19.25 5.2 52687 52658 20 -4
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 1.62 1.63 100 100 0.466 2.25 4.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1R9G CHAIN A 1.62 25 52656 2676 99.941 0.153 0.153 0.1515 0.1648 0.1892 0.1994 19.129
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] 0.214 -0.161 0.309 -0.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.325 r_dihedral_angle_4_deg 16.78 r_dihedral_angle_3_deg 13.705 r_dihedral_angle_1_deg 6.943 r_scangle_it 4.421 r_scbond_it 3.584 r_scangle_other 2.258 r_mcangle_it 2.179 r_mcbond_it 2.029 r_angle_refined_deg 1.962
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.325 r_dihedral_angle_4_deg 16.78 r_dihedral_angle_3_deg 13.705 r_dihedral_angle_1_deg 6.943 r_scangle_it 4.421 r_scbond_it 3.584 r_scangle_other 2.258 r_mcangle_it 2.179 r_mcbond_it 2.029 r_angle_refined_deg 1.962 r_scbond_other 1.333 r_angle_other_deg 1.056 r_mcangle_other 1.024 r_mcbond_other 0.385 r_nbd_refined 0.279 r_symmetry_hbond_refined 0.262 r_symmetry_vdw_other 0.234 r_xyhbond_nbd_refined 0.228 r_nbd_other 0.226 r_symmetry_vdw_refined 0.223 r_nbtor_refined 0.188 r_chiral_restr 0.127 r_nbtor_other 0.089 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3483 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction