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X-ray Crystal structure of a methylmalonate semialdehyde dehydrogenase from Pseudomonas sp. AAC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 281 Protein at 5 mg/mL with added acetyl-CoA; crystal conditions were 100 mM bis-tris propane at pH 7.6, 24% PEG 3350, 210 mM trisodium citr
ate in 150 plus 150 nL drops.
Crystal Properties Matthews coefficient Solvent content 2.54 51.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.891 α = 90 b = 156.631 β = 90 c = 192.246 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 ADSC QUANTUM 315 2015-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.95 49.6 99.9 0.178 0.998 11.5 14.7 74332
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.01 100 1.607 0.818 2 15
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 4zz7 2.95 49 70516 3714 99.86 0.21417 0.21236 0.2156 0.24862 0.2511 RANDOM 72.029
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] -4.13 7.93 -3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_4_deg 19.73 r_dihedral_angle_3_deg 17.191 r_long_range_B_refined 14.274 r_long_range_B_other 14.274 r_scangle_other 8.656 r_mcangle_other 8.043 r_mcangle_it 8.042 r_dihedral_angle_1_deg 5.984 r_scbond_it 5.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_4_deg 19.73 r_dihedral_angle_3_deg 17.191 r_long_range_B_refined 14.274 r_long_range_B_other 14.274 r_scangle_other 8.656 r_mcangle_other 8.043 r_mcangle_it 8.042 r_dihedral_angle_1_deg 5.984 r_scbond_it 5.306 r_scbond_other 5.306 r_mcbond_it 5.171 r_mcbond_other 5.166 r_angle_refined_deg 1.686 r_angle_other_deg 1.058 r_chiral_restr 0.106 r_bond_refined_d 0.012 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 20813 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing