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E. coli L-aspartate-alpha-decarboxylase mutant N72Q to a resolution of 1.9 Angstroms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AW8 PDB ENTRY 1AW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 ADC.PANZ COMPLEX WAS PREPARED IN A 10: 11 RATIO AT A FINAL CONCENTRATION OF 5.7 MG/ML WITH A 2-FOLD MOLAR EXCESS (RELATIVE TO PANZ) OF ACETYLCOA IN 0.05 M TRIS-HCL PH 7.69, 0.1 M NACL, 0.1 MM DTT. THIS WAS MIXED IN A 1:1 RATIO WITH RESERVOIR SOLUTION (0.2 M POTASSIUM THIOCYANATE, 0.1 M BIS- TRIS PROPANE PH 6.8, 20 % W/V PEG 3350) AND CRYSTALLIZED BY HANGING DROP VAOUR DIFFUSION (4 UL DROPLET OVER A 1 ML RESERVOIR).
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.35 α = 90 b = 71.35 β = 90 c = 112.31 γ = 90
Symmetry Space Group I 4 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 IMAGE PLATE RIGAKU IMAGE PLATE VARIMAX 2014-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.9 23.26 99.9 0.14 9.9 6.4 11805 10.3
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 1.9 1.94 100 0.64 2.6 5.8
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 PDB ENTRY 1AW8 1.9 60.22 11235 552 99.75 0.18894 0.18622 0.1959 0.24418 0.2558 RANDOM 24.788
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] 0.6 0.6 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.232 r_dihedral_angle_3_deg 14.51 r_dihedral_angle_4_deg 10.197 r_dihedral_angle_1_deg 6.636 r_scbond_it 3.244 r_mcangle_it 2.968 r_mcbond_it 2.039 r_mcbond_other 2.029 r_angle_refined_deg 1.737 r_angle_other_deg 0.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.232 r_dihedral_angle_3_deg 14.51 r_dihedral_angle_4_deg 10.197 r_dihedral_angle_1_deg 6.636 r_scbond_it 3.244 r_mcangle_it 2.968 r_mcbond_it 2.039 r_mcbond_other 2.029 r_angle_refined_deg 1.737 r_angle_other_deg 0.826 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 942 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing