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Malate dehydrogenase from Methylobacterium extorquens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GVH
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
Crystal Properties Matthews coefficient Solvent content 2.66 53.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.995 α = 90 b = 108.995 β = 90 c = 104.659 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 ADSC QUANTUM 315r 2014-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.127092 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.66 37.75 99.6 14.2 11.2 44052
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 3gvh 1.66 37.75 41822 2191 99.59 0.14084 0.1395 0.1393 0.16765 0.168 RANDOM 21.927
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] 0.32 0.16 0.32 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.427 r_dihedral_angle_4_deg 23.546 r_dihedral_angle_3_deg 13.047 r_long_range_B_refined 6.688 r_long_range_B_other 6.218 r_dihedral_angle_1_deg 5.817 r_scangle_other 4.518 r_mcangle_it 3.055 r_mcangle_other 3.055 r_scbond_it 2.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.427 r_dihedral_angle_4_deg 23.546 r_dihedral_angle_3_deg 13.047 r_long_range_B_refined 6.688 r_long_range_B_other 6.218 r_dihedral_angle_1_deg 5.817 r_scangle_other 4.518 r_mcangle_it 3.055 r_mcangle_other 3.055 r_scbond_it 2.919 r_scbond_other 2.918 r_mcbond_it 2.097 r_mcbond_other 2.097 r_angle_refined_deg 1.909 r_angle_other_deg 1.069 r_chiral_restr 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 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 2323 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing