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Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BDM PDB entry 1bdm_A as per MorDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Microlytics MCSG1 screen, condition H11: 25% PEG 3350, 200mM NaCl, 100mM HEPES / NaOH pH 7.5: NafoA.00005.a.B1.PS38166 at 16.9mg/ml + 2mM NAD. Cryo: 15% EG: tray: 298888 h11: puck eqq6-5.
Crystal Properties Matthews coefficient Solvent content 1.97 37.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.33 α = 91.093 b = 137.48 β = 89.998 c = 139.28 γ = 91.482
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 RAYONIX MX-300 2018-03-01 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) 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 2.05 44.23 96.7 0.085 0.108 0.997 8.18 2.645 271476 23.36
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 2.05 2.1 96.1 0.512 0.65 0.869 2.01 2.656
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 1bdm_A as per MorDa 2.05 44.23 1.98 270670 1853 96.45 0.2108 0.2106 0.2106 0.2324 0.2349 0 33.15
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 17.1479 f_angle_d 0.8406 f_chiral_restr 0.0543 f_bond_d 0.0069 f_plane_restr 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28960 Nucleic Acid Atoms Solvent Atoms 2237 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing ARP/wARP model building BUCCANEER model building