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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 wild-type MSAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 61.5% (v/v) MPD, 100 mM Tris-Cl buffer (pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.889 α = 90 b = 51.889 β = 90 c = 219.083 γ = 120
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 210 2004-08-04 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) R Sym 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 1.6 72.55 98.8 0.144 0.127 3.5 5.2 87168 86122 2 11.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.68 96.5 0.413 0.316 2.2 2.7 12281
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 (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 wild-type MSAD 1.65 72.55 74759 74759 3904 99.04 0.18641 0.18366 0.1885 0.23867 0.1811 RANDOM 11.624
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] -0.01 -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.301 r_sphericity_free 4.473 r_scangle_it 2.998 r_angle_refined_deg 2.485 r_scbond_it 2.053 r_rigid_bond_restr 1.51 r_mcangle_it 1.495 r_sphericity_bonded 1.209 r_mcbond_it 0.993 r_symmetry_vdw_refined 0.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.301 r_sphericity_free 4.473 r_scangle_it 2.998 r_angle_refined_deg 2.485 r_scbond_it 2.053 r_rigid_bond_restr 1.51 r_mcangle_it 1.495 r_sphericity_bonded 1.209 r_mcbond_it 0.993 r_symmetry_vdw_refined 0.376 r_symmetry_hbond_refined 0.371 r_xyhbond_nbd_refined 0.242 r_nbd_refined 0.241 r_chiral_restr 0.154 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5992 Nucleic Acid Atoms Solvent Atoms 956 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement