☰ Navigation Tabs
2.15 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HHP PDB entry 3HHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 20.0 mg/mL protein in 0.3 M sodium chloride, 0.01 M HEPES, pH 7.5, screen: 0.1 M lithium sulfate, 0.1 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 20% w/v PEG3350, 0.25 mM D-Malic acid, cryoprotectant: paratone
Crystal Properties Matthews coefficient Solvent content 2.09 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.688 α = 90 b = 94.119 β = 121.7 c = 73.215 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER X 9M Si(111) 2017-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07822 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.15 30 97.5 0.122 0.122 0.039 18.5 10.9 33055 -3 34.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 99.3 0.749 0.749 0.229 0.876 4.3 11.4
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 3HHP 2.15 29.68 31307 1660 97.44 0.18516 0.18236 0.1918 0.23732 0.2498 RANDOM 49.215
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] 5.85 2.49 -3.33 -3.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.656 r_dihedral_angle_4_deg 10.18 r_dihedral_angle_3_deg 8.844 r_long_range_B_refined 6.704 r_long_range_B_other 6.637 r_scangle_other 3.228 r_mcangle_it 2.963 r_mcangle_other 2.963 r_dihedral_angle_1_deg 2.192 r_scbond_it 2.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.656 r_dihedral_angle_4_deg 10.18 r_dihedral_angle_3_deg 8.844 r_long_range_B_refined 6.704 r_long_range_B_other 6.637 r_scangle_other 3.228 r_mcangle_it 2.963 r_mcangle_other 2.963 r_dihedral_angle_1_deg 2.192 r_scbond_it 2.014 r_scbond_other 2.001 r_mcbond_it 1.903 r_mcbond_other 1.9 r_angle_refined_deg 1.429 r_angle_other_deg 0.879 r_chiral_restr 0.078 r_gen_planes_refined 0.023 r_gen_planes_other 0.02 r_bond_refined_d 0.009 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 4662 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing