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Crystal Structures of the Wild-type, Mutant-P1A and Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis for the Decarboxylase and Hydratase Activities
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other wildtype MSAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 2.8 M Li(CH3COO), 0.7 M (NH4)2SO4, and 100 mM sodium citrate buffer (pH 5.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.152 α = 90 b = 110.152 β = 90 c = 110.152 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2003-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.74 29.4 99.4 0.129 9.2 12.4 12097 11976 2 38.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.74 2.86 98.7 0.391 1188
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 wildtype MSAD 2.74 29.4 11328 11251 623 99.32 0.1641 0.1641 0.1614 0.1655 0.2133 0.1686 RANDOM 31.56
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.792 r_sphericity_free 3.599 r_scangle_it 3.292 r_scbond_it 1.989 r_angle_refined_deg 1.923 r_mcangle_it 1.417 r_rigid_bond_restr 1.113 r_sphericity_bonded 1.105 r_mcbond_it 0.789 r_symmetry_hbond_refined 0.215
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.792 r_sphericity_free 3.599 r_scangle_it 3.292 r_scbond_it 1.989 r_angle_refined_deg 1.923 r_mcangle_it 1.417 r_rigid_bond_restr 1.113 r_sphericity_bonded 1.105 r_mcbond_it 0.789 r_symmetry_hbond_refined 0.215 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.198 r_symmetry_vdw_refined 0.172 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1974 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement