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Crystal structure of phosphoglycerate mutase from Naegleria fowleri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E58 1e58, found by Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 Micolytic MCSG1 A7: 200mM MgCl2, 25% PEG 3350, 100mM BisTris HCl pH 5.5:NafoA.0013.a.B1.PS38236 at 18.9mg/ml: crystals soaked for 3h with 2.5mM 3-Pospho-glycerate (BSI 1959, not visible in structure): cryo: 20% EG, tray: 290723a7, puck wvn8-2
Crystal Properties Matthews coefficient Solvent content 2.28 46.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.61 α = 90 b = 89.33 β = 90 c = 157.88 γ = 90
Symmetry Space Group I 2 2 2
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+ RIGAKU VARIMAX 2016-05-01 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) Rrim I (All) CC (Half) 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 1.7 47.046 99.3 0.042 0.044 1 34.11 12.494 60168 -3 19.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 93.1 0.431 0.473 0.947 3.69 5.942
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1e58, found by Morda 1.7 47.046 1.34 60142 2059 99.22 0.1659 0.1649 0.1947 0.1866 RANDOM 27.7416
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.544 f_angle_d 0.928 f_chiral_restr 0.057 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3965 Nucleic Acid Atoms Solvent Atoms 605 Heterogen Atoms 29
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MoRDa phasing PHENIX model building Coot model building PHENIX refinement PDB_EXTRACT data extraction