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Crystal structure of PbgP3 protein from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z7E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 protein at 8.2 mg/mL against PACT screen condition C10, 20% PEG 6000, 0.2 M MgCl2, 0.1 M Hepes, 20% ethylene glycol as cryo-protection reagent, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.57 α = 90 b = 91.55 β = 91.63 c = 147.26 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 2011-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 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 2.1 50 99 0.06 14.24 2.8 129532 128239 -3 34.447
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 2.1 2.15 99.4 0.428 2.23 2.8 9518
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 1z7e 2.1 50 128096 6444 98.9 0.1793 0.177 0.1824 0.2213 0.2273 RANDOM 30.9176
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] 2.9 1.27 -0.87 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.611 r_dihedral_angle_4_deg 15.778 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_1_deg 5.687 r_scangle_it 3.413 r_scbond_it 2.132 r_angle_refined_deg 1.307 r_mcangle_it 1.269 r_mcbond_it 0.703 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.611 r_dihedral_angle_4_deg 15.778 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_1_deg 5.687 r_scangle_it 3.413 r_scbond_it 2.132 r_angle_refined_deg 1.307 r_mcangle_it 1.269 r_mcbond_it 0.703 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15337 Nucleic Acid Atoms Solvent Atoms 881 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction