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Malate dehydrogenase from Methylobacterium extorquens, complexed with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ROP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 25-28% PEG400, 180-220mM CaCl2, 0.1M Hepes pH 7.5, soaked with 1mM NAD
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.189 α = 90 b = 108.189 β = 90 c = 104.321 γ = 120
Symmetry Space Group P 64 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 RAYONIX MX-300 2015-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.53 54.09 100 0.108 0.033 0.998 12.1 10.6 54696
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.56 99.8 0.8 0.357 0.733 2.2 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 4rop 1.53 54.09 51855 2774 99.88 0.12628 0.12364 0.1377 0.17726 0.1841 RANDOM 24.517
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] 0.41 0.2 0.41 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.203 r_dihedral_angle_4_deg 17.4 r_sphericity_free 16.634 r_sphericity_bonded 14.779 r_dihedral_angle_3_deg 11.789 r_dihedral_angle_1_deg 5.615 r_scangle_other 5.076 r_long_range_B_refined 5.046 r_long_range_B_other 4.722 r_scbond_other 4.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.203 r_dihedral_angle_4_deg 17.4 r_sphericity_free 16.634 r_sphericity_bonded 14.779 r_dihedral_angle_3_deg 11.789 r_dihedral_angle_1_deg 5.615 r_scangle_other 5.076 r_long_range_B_refined 5.046 r_long_range_B_other 4.722 r_scbond_other 4.443 r_scbond_it 4.439 r_rigid_bond_restr 4.333 r_mcangle_it 3.323 r_mcangle_other 3.322 r_mcbond_other 2.806 r_mcbond_it 2.805 r_angle_refined_deg 1.791 r_angle_other_deg 1.033 r_chiral_restr 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2294 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing