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crystal structure of the S133A mutant of Malonamidase E2 complexed with malonate from Bradyrhizobium japonicum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GR8 PDB ENTRY 1GR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20% POLYETHYLENE GLYCOL 1000, 0.1 M TRIS-HCL, PH 7.0
Crystal Properties Matthews coefficient Solvent content 2 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.629 α = 90 b = 95.225 β = 90 c = 74.981 γ = 90
Symmetry Space Group P 21 21 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 CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B PAL/PLS 6B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 52.083 92.1 0.055 7.16 5.07 46861 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION DIRECT METHODS THROUGHOUT PDB ENTRY 1GR8 2 52 1 46834 92.1 0.188 0.188 0.245 RANDOM
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 c_angle_deg 1.271 c_bond_d 0.0052 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.271 c_bond_d 0.0052 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6122 Nucleic Acid Atoms Solvent Atoms 913 Heterogen Atoms 14
Software Software Software Name Purpose CNS refinement SMART data reduction PROSCALE data scaling CNS phasing