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Crystal structure of nicotinate-nucleotide pyrophosphorylase from Burkholderi pseudomallei
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 HAMPTON CRYSTAL SCREEN CONDITION E8, 1.5 M NACL,
10% ETHANOL WITH 25% GLYCEROL AS CRYO-PROTECTANT,
28.7 MG/ML PROTEIN, CRYSTAL ID 109334E8,
VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties Matthews coefficient Solvent content 2.27 45.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.978 α = 90 b = 57.414 β = 106.74 c = 66.243 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 2008-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 2.25 50 98.9 0.068 21.998 3.8 27262
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) 2.25 2.33 97.7 0.589 2.27 3.7 2650
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.25 39.14 27260 1366 98.67 0.217 0.214 0.2132 0.273 0.2687 RANDOM 48.358
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] 1.08 2.07 -2.44 2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.522 r_dihedral_angle_4_deg 19.676 r_dihedral_angle_3_deg 19.167 r_dihedral_angle_1_deg 6.585 r_scangle_it 4.725 r_scbond_it 2.895 r_mcangle_it 2.016 r_angle_refined_deg 1.791 r_mcbond_it 1.101 r_angle_other_deg 1.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.522 r_dihedral_angle_4_deg 19.676 r_dihedral_angle_3_deg 19.167 r_dihedral_angle_1_deg 6.585 r_scangle_it 4.725 r_scbond_it 2.895 r_mcangle_it 2.016 r_angle_refined_deg 1.791 r_mcbond_it 1.101 r_angle_other_deg 1.074 r_mcbond_other 0.232 r_chiral_restr 0.109 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3776 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling