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Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 3-phosphoglyceric acid and vanadate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 Emerald Cryo B-4, 100MM MES PH 7.5, 5% PEG 1000, 10% GLYCEROL, 30% PEG 600, 11.7 mg/mL protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.749 α = 105.46 b = 48.983 β = 91.15 c = 62.96 γ = 107.42
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 RIGAKU SATURN 944 2008-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 94.5 0.068 13.141 2 21960
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 2.25 2.33 82.1 0.245 3.452 1.9 1899
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 50 21960 1121 94.24 0.174 0.171 0.1726 0.234 0.1879 RANDOM 22.897
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] 0.55 0.17 -1.05 -0.8 0.5 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.877 r_dihedral_angle_4_deg 17.728 r_dihedral_angle_3_deg 14.811 r_dihedral_angle_1_deg 7.139 r_scangle_it 3.694 r_scbond_it 2.4 r_angle_refined_deg 1.754 r_mcangle_it 1.453 r_angle_other_deg 0.973 r_mcbond_it 0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.877 r_dihedral_angle_4_deg 17.728 r_dihedral_angle_3_deg 14.811 r_dihedral_angle_1_deg 7.139 r_scangle_it 3.694 r_scbond_it 2.4 r_angle_refined_deg 1.754 r_mcangle_it 1.453 r_angle_other_deg 0.973 r_mcbond_it 0.818 r_mcbond_other 0.211 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3771 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 73
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