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Structure of Alpha-Glycerophosphate Oxidase from Streptococcus sp.: A Template for the Mitochondrial Alpha-Glycerophosphate Dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RGH PDB entry 2RGH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 PEG 1000, Tris, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.94 58.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.363 α = 90 b = 106.785 β = 99.18 c = 58.887 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9296 CHESS F1
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 2.4 28.89 0.064 9.9 54822
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) 2.4 2.53 0.298 2.8 8692
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-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 2RGH 2.4 12 54822 2938 94.87 0.23808 0.23808 0.23759 0.2297 0.24708 0.274 RANDOM 62.886
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] 0.02 0.04 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.125 r_dihedral_angle_4_deg 17.634 r_dihedral_angle_3_deg 15.517 r_scangle_it 3.237 r_dihedral_angle_1_deg 3.101 r_mcangle_it 2.539 r_scbond_it 2.173 r_angle_refined_deg 1.675 r_mcbond_it 1.457 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.125 r_dihedral_angle_4_deg 17.634 r_dihedral_angle_3_deg 15.517 r_scangle_it 3.237 r_dihedral_angle_1_deg 3.101 r_mcangle_it 2.539 r_scbond_it 2.173 r_angle_refined_deg 1.675 r_mcbond_it 1.457 r_nbtor_refined 0.328 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.276 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.111 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8524 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 106
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling