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Crystal structure of a Glutamine-binding periplasmic protein from Burkholderia pseudomallei in complex with glutamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GGG pdb entry 1ggg modified with CCP4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 MD Morpheus screen C12: 12.5% PEG 3350, 12.5% PEG 1000, 12.5% MPD, 30mM sodium nitrate, 30mM disodium hydrgon phosphate, 30mM ammonium sulphate, 100mM bicine/trizma; BupsA.17285.b.A2 PW PS01148 20mg/ml, tray 232242c12, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.27 45.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.33 α = 90 b = 74.5 β = 100.63 c = 60.19 γ = 90
Symmetry Space Group P 1 21 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 315r 2012-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 2.4 50 99.9 0.086 14.36 3.8 19275 19249 -3 37.414
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 2.4 2.46 99.6 0.524 2.6 3.8
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 (All) 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 1ggg modified with CCP4 program chainsaw 2.4 50 19249 19235 986 99.93 0.1789 0.1789 0.1769 0.1779 0.2152 0.2157 RANDOM 30.518
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] -0.35 0.5 0.3 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.528 r_dihedral_angle_4_deg 18.63 r_dihedral_angle_3_deg 13.939 r_dihedral_angle_1_deg 6.272 r_angle_refined_deg 1.588 r_angle_other_deg 1.166 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.528 r_dihedral_angle_4_deg 18.63 r_dihedral_angle_3_deg 13.939 r_dihedral_angle_1_deg 6.272 r_angle_refined_deg 1.588 r_angle_other_deg 1.166 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3345 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction