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Crystal structure of Glycine Oxidase G51S/A54R/H244A mutant in complex with inhibitor glycolate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RYI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100mM Hepes/Na, pH 7.5, 28 % w/v PEG 400, 200mM CaCl2, 30mM glycolate/Na, 3 % glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.344 α = 90 b = 215.058 β = 90 c = 217.083 γ = 90
Symmetry Space Group C 2 2 21
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 RAYONIX MX-225 2009-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 1.04063 BESSY 14.2
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 76.25 0.086 10.1 52481 3 43.993
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 2.74 100 0.344 10.7 10.1
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) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1RYI 2.6 76.25 49195 2639 98.76 0.19866 0.19561 0.25654 0.2482 RANDOM 30.946
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] -1.18 1.02 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.009 r_dihedral_angle_3_deg 16.923 r_dihedral_angle_4_deg 16.138 r_dihedral_angle_1_deg 6.027 r_scangle_it 1.966 r_angle_refined_deg 1.309 r_scbond_it 1.199 r_mcangle_it 1.094 r_mcbond_it 0.611 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.009 r_dihedral_angle_3_deg 16.923 r_dihedral_angle_4_deg 16.138 r_dihedral_angle_1_deg 6.027 r_scangle_it 1.966 r_angle_refined_deg 1.309 r_scbond_it 1.199 r_mcangle_it 1.094 r_mcbond_it 0.611 r_nbtor_refined 0.309 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.209 r_symmetry_vdw_refined 0.202 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11332 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 232
Software Software Software Name Purpose MxCuBE data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing