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MDH3 wild type, nad-oaa-form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MLD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% (w/v) PEG 10000, 0.1M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.218 α = 90 b = 86.658 β = 90 c = 135.05 γ = 90
Symmetry Space Group P 21 21 21
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 MX300HE 2018-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 99.9 0.028 40 7 40043 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 0.186 5.7 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1MLD 2.1 47.75 37905 2015 99.66 0.19911 0.19559 0.26591 0.2623 RANDOM 40.391
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] 0.15 -0.17 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.793 r_dihedral_angle_4_deg 19.812 r_dihedral_angle_3_deg 17.153 r_long_range_B_refined 7.017 r_long_range_B_other 7.017 r_dihedral_angle_1_deg 6.676 r_scangle_other 5.3 r_mcangle_other 4.552 r_mcangle_it 4.549 r_scbond_it 3.554
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.793 r_dihedral_angle_4_deg 19.812 r_dihedral_angle_3_deg 17.153 r_long_range_B_refined 7.017 r_long_range_B_other 7.017 r_dihedral_angle_1_deg 6.676 r_scangle_other 5.3 r_mcangle_other 4.552 r_mcangle_it 4.549 r_scbond_it 3.554 r_scbond_other 3.554 r_mcbond_it 3.208 r_mcbond_other 3.201 r_angle_refined_deg 1.91 r_angle_other_deg 1.06 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5164 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing