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X-ray crystal structure of Aspartate alpha-decarboxylase in complex with D-Serine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AW8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.5 293 1.8 M ammonium sulphate,
100 mM sodium citrate pH 4.5
Crystal Properties Matthews coefficient Solvent content 3.11 60.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.3 α = 90 b = 71.3 β = 90 c = 216.65 γ = 120
Symmetry Space Group P 61 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 PIXEL DECTRIS PILATUS 6M 2010-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9778 Diamond I24
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 1.75 46.98 99.99 0.02384 0.99 21.5 2 33922
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 1.75 1.81 0.1564 0.93 5.25
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1AW8 1.75 46.975 33922 1702 99.988 0.171 0.1705 0.1809 0.1905 0.1996 20.673
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] 0.257 0.129 0.257 -0.835
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.113 r_dihedral_angle_1_deg 16.825 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_4_deg 9.698 r_lrange_it 5.322 r_lrange_other 5.321 r_scangle_it 2.158 r_scangle_other 2.157 r_mcangle_it 1.939 r_mcangle_other 1.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.113 r_dihedral_angle_1_deg 16.825 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_4_deg 9.698 r_lrange_it 5.322 r_lrange_other 5.321 r_scangle_it 2.158 r_scangle_other 2.157 r_mcangle_it 1.939 r_mcangle_other 1.939 r_scbond_it 1.317 r_scbond_other 1.317 r_angle_refined_deg 1.258 r_angle_other_deg 1.244 r_mcbond_it 1.111 r_mcbond_other 1.111 r_nbd_other 0.246 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.208 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_other 0.158 r_symmetry_xyhbond_nbd_refined 0.151 r_nbtor_refined 0.148 r_xyhbond_nbd_refined 0.139 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.053 r_bond_refined_d 0.004 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1828 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing