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2.1 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae in Complex with L-Malate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 Protein: 20.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5;
Screen: 0.2M Ammonium formate, 20% (w/v) PEG3350, 0.25mM DL-Malic acid;
Cryo: paratone.
Crystal Properties Matthews coefficient Solvent content 1.9 35.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.108 α = 71.09 b = 78.079 β = 75.44 c = 114.029 γ = 68.06
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 300 mm CCD C(111) 2017-04-20 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) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 30 98.2 0.093 0.093 0.108 0.054 13.4 4 126522 -3 28.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 97.2 0.662 0.662 0.77 0.392 0.665 2.1 3.9
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 3HHP 2.1 29.75 120245 6277 97.85 0.17202 0.16958 0.1754 0.21869 0.2202 RANDOM 35.765
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] -0.55 -0.88 -0.44 0.27 0.77 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.698 r_dihedral_angle_4_deg 12.609 r_dihedral_angle_3_deg 9.068 r_long_range_B_refined 4.753 r_long_range_B_other 4.687 r_dihedral_angle_1_deg 2.403 r_scangle_other 2.403 r_mcangle_it 2.138 r_mcangle_other 2.138 r_scbond_it 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.698 r_dihedral_angle_4_deg 12.609 r_dihedral_angle_3_deg 9.068 r_long_range_B_refined 4.753 r_long_range_B_other 4.687 r_dihedral_angle_1_deg 2.403 r_scangle_other 2.403 r_mcangle_it 2.138 r_mcangle_other 2.138 r_scbond_it 1.453 r_scbond_other 1.453 r_angle_refined_deg 1.359 r_mcbond_it 1.279 r_mcbond_other 1.279 r_angle_other_deg 0.863 r_chiral_restr 0.076 r_gen_planes_refined 0.022 r_gen_planes_other 0.02 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18305 Nucleic Acid Atoms Solvent Atoms 1280 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing