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Crystal structure of pyridoxal phosphate biosynthetic protein from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M5W PDB entry 1M5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 16.4% PEG4000, 0.1 M Hepes NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.29 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.09 α = 118.48 b = 91.864 β = 116.81 c = 90.024 γ = 93.5
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 2008-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97934 APS 24-ID-E
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 2.28 50 96.5 0.107 12.627 3.7 91137
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 2.28 2.38 85.2 0.481 2.1 3 8058
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1M5W 2.28 46.5 91104 4580 94.2 0.189 0.186 0.245 0.225 RANDOM 28.325
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] -0.58 0.93 -0.84 0.49 -0.65 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.406 r_dihedral_angle_4_deg 19.242 r_dihedral_angle_3_deg 15.597 r_dihedral_angle_1_deg 5.375 r_scangle_it 2.423 r_scbond_it 1.389 r_angle_refined_deg 1.152 r_mcangle_it 0.91 r_angle_other_deg 0.894 r_mcbond_it 0.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.406 r_dihedral_angle_4_deg 19.242 r_dihedral_angle_3_deg 15.597 r_dihedral_angle_1_deg 5.375 r_scangle_it 2.423 r_scbond_it 1.389 r_angle_refined_deg 1.152 r_mcangle_it 0.91 r_angle_other_deg 0.894 r_mcbond_it 0.469 r_mcbond_other 0.077 r_chiral_restr 0.065 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14763 Nucleic Acid Atoms Solvent Atoms 851 Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling