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Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with vanadate and glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 Emerald Cryo Screen B-4, 100 mM MES pH 6.0, 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 43.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.175 α = 106.42 b = 49.112 β = 91.18 c = 62.59 γ = 107.61
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 2008-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 1.93 50 92.8 0.066 21.975 3.4 34058
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 1.93 2 80.4 0.301 2.89 2.2 2972
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 3EZN 1.93 50 34057 1696 92.62 0.189 0.187 0.1923 0.227 0.2003 RANDOM 22.537
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 0.31 -0.28 -0.38 0.17 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.778 r_dihedral_angle_4_deg 18.038 r_dihedral_angle_3_deg 12.783 r_dihedral_angle_1_deg 6.004 r_scangle_it 2.505 r_scbond_it 1.511 r_angle_refined_deg 1.2 r_mcangle_it 1.019 r_angle_other_deg 0.838 r_mcbond_it 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.778 r_dihedral_angle_4_deg 18.038 r_dihedral_angle_3_deg 12.783 r_dihedral_angle_1_deg 6.004 r_scangle_it 2.505 r_scbond_it 1.511 r_angle_refined_deg 1.2 r_mcangle_it 1.019 r_angle_other_deg 0.838 r_mcbond_it 0.55 r_mcbond_other 0.115 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3666 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 82
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