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CRYSTAL STRUCTURE AND MECHANISM OF L-ARGININE: GLYCINE AMIDINOTRANSFERASE: A MITOCHONDRIAL ENZYME INVOLVED IN CREATINE BIOSYNTHESIS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JDW PDB ENTRY 1JDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1 PART OF AT38H (13-16 MG/ML) 2 PARTS OF PRECIPITANT (3% PEG 6000, 40 MM HEPES, 1MM GLUTATHIONE, PH7.0), SEVERAL DAYS AT ROOM TEMPERATURE, MACRO SEEDING.
L-ARGININE WAS SOAKED INTO CRYSTAL AND IS BOUND TO ACTIVE
SITE.
Crystal Properties Matthews coefficient Solvent content 3.8 65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.78 α = 90 b = 83.78 β = 90 c = 199.45 γ = 90
Symmetry Space Group P 43 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 290 IMAGE PLATE MARRESEARCH 1995-12-26 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R
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 2.5 8 87.2 0.081 3.76 22282
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) 2.5 2.53 81.3 0.261 3.7
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-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION ISOMORPHOUS WITH PDB ENTRY 1JDW FREE R PDB ENTRY 1JDW 2.5 8 21405 87.2 0.183 0.183 23.58
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 x_dihedral_angle_d 25.3 x_angle_deg 1.684 x_improper_angle_d 1.54 x_bond_d 0.012 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.3 x_angle_deg 1.684 x_improper_angle_d 1.54 x_bond_d 0.012 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2940 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 11
Software Software Software Name Purpose MOSFLM data reduction ROTAVATA/AGROVATA data reduction X-PLOR model building X-PLOR refinement CCP4 data scaling ROTAVATA data scaling X-PLOR phasing