☰ Navigation Tabs
Crystal structure of a phosphoglycerate mutase gpmA from Borrelia burgdorferi B31
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LNT PDB ENTRY 3LNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 BobuA.01013.a.A1 selenomethionine-labeled PW26571 at 27.7 mg/mL against CSHT B6: 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, 20% PEG8000, cryoprotectant: 20% ethylene glycol, crystal tracking ID 232024b6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.88 57.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.32 α = 90 b = 116.75 β = 107.67 c = 84.41 γ = 90
Symmetry Space Group P 1 21 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 CCD MARMOSAIC 225 mm CCD 2012-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.3 50 99.9 0.078 18.97 7.7 63486 63406 -3 42.001
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 2.3 2.36 99.9 0.473 4.78
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 PDB ENTRY 3LNT 2.3 50 63405 3216 99.97 0.1775 0.1762 0.1782 0.2013 0.1998 RANDOM 38.1379
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] -1.52 -0.2 2.26 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.567 r_dihedral_angle_4_deg 15.953 r_dihedral_angle_3_deg 13.229 r_dihedral_angle_1_deg 5.685 r_angle_refined_deg 1.442 r_angle_other_deg 1.174 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.567 r_dihedral_angle_4_deg 15.953 r_dihedral_angle_3_deg 13.229 r_dihedral_angle_1_deg 5.685 r_angle_refined_deg 1.442 r_angle_other_deg 1.174 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7600 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 13
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction