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Crystal Structure of L-Glutamate Oxidase from Streptomyces sp. X-119-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8R PDB ENTRY 1F8R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 278 100mM CAPS-buffer, 1200mM NaH2PO4, 800mM K2HPO4, 50mM LiSO4, 5mM DTT, 20mM KPB, 10mg/ml GOX, pH 10.50, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.39 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.875 α = 90 b = 123.875 β = 90 c = 168.762 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 IMAGE PLATE RIGAKU RAXIS V 2004-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL24XU SPring-8 BL24XU
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 2.6 50 100 0.08 34.043 10 24388 75.5
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 2.6 2.69 100 0.489 4.779 9.8
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 PDB ENTRY 1F8R 2.8 45.27 19457 19146 929 98.4 0.248 0.248 0.2381 0.308 0.2947 RANDOM 34.3
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_dihedral_angle_d 23 c_angle_deg 1.5 c_improper_angle_d 0.96 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_angle_deg 1.5 c_improper_angle_d 0.96 c_bond_d 0.008 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_na c_dihedral_angle_d_prot 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 4739 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 68
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling