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Crystal structure of Indole-3-glycerol phosphate synthase from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PII PDB entry 1pii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 Internal tracking number 223543D9. Crystallant (JCSG D9): 25.5% PEG 4000, 15% glycerol, 170 mM Ammonium Sulfate. Protein: BrabA.17351.a.A1 PS01096 at 63 mg/ml in a buffer consisting of 25 mM HEPES, 300-500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.68 54.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.8 α = 90 b = 73.29 β = 90 c = 118.94 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 315 2011-09-09 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 2.15 50 99.9 0.109 13.57 7.3 34823 -3 30.856
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 2.15 2.21 100 0.469 4.2 7.4
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 MR THROUGHOUT PDB entry 1pii 2.15 50 34822 1751 99.89 0.185 0.183 0.1861 0.228 0.2269 RANDOM 26.438
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] -0.56 -1.14 1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.019 r_dihedral_angle_4_deg 21.075 r_dihedral_angle_3_deg 13.068 r_dihedral_angle_1_deg 5.195 r_angle_refined_deg 1.524 r_angle_other_deg 1.166 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.019 r_dihedral_angle_4_deg 21.075 r_dihedral_angle_3_deg 13.068 r_dihedral_angle_1_deg 5.195 r_angle_refined_deg 1.524 r_angle_other_deg 1.166 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3905 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 28
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction