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Crystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X19 1x19 modified with ccp4 chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 EMERALD CRYO B-4: 100MM MES PH 6.0, 5% PEG 1000, 10% GLYCEROL, 30% PEG 600, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 298K, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.06 40.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.94 α = 107.11 b = 49.08 β = 91.19 c = 62.11 γ = 107.81
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 SATURN 944 2008-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 93.7 0.041 0.041 25.7 3.74 26261 26261 -3 22.93
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 83.2 0.137 0.137 9.9 3.6 1736
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1x19 modified with ccp4 chainsaw 2.1 50 26261 26261 1315 93.8 0.152 0.152 0.15 0.1555 0.204 0.2057 RANDOM 14.88
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] 0.49 0.36 -0.4 -0.15 0.18 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.452 r_dihedral_angle_4_deg 16.651 r_dihedral_angle_3_deg 13.351 r_dihedral_angle_1_deg 6.721 r_scangle_it 4.29 r_scbond_it 2.737 r_mcangle_it 1.69 r_angle_refined_deg 1.65 r_angle_other_deg 0.979 r_mcbond_it 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.452 r_dihedral_angle_4_deg 16.651 r_dihedral_angle_3_deg 13.351 r_dihedral_angle_1_deg 6.721 r_scangle_it 4.29 r_scbond_it 2.737 r_mcangle_it 1.69 r_angle_refined_deg 1.65 r_angle_other_deg 0.979 r_mcbond_it 0.96 r_mcbond_other 0.275 r_chiral_restr 0.106 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3703 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 37
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling