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Crystal structure of glyceraldehyde oxidoreductase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FFV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1 MNa-acetate, 0.2M CH3COONH4, 15% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.75 55.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.431 α = 90 b = 143.431 β = 90 c = 235.509 γ = 120
Symmetry Space Group P 65 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 CCD ADSC QUANTUM 4r 2003-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL40B2 1.0 SPring-8 BL40B2
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 2.2 50 100 0.078 36.7 12.1 73074
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 2.2 2.28 100 0.394 6.9 12.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FFV 2.2 41.4 69288 3679 99.9 0.17998 0.17671 0.1774 0.24231 0.2429 RANDOM 32.736
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 r_dihedral_angle_2_deg 37.848 r_dihedral_angle_4_deg 18.224 r_dihedral_angle_3_deg 17.436 r_long_range_B_refined 7.179 r_dihedral_angle_1_deg 7.057 r_scbond_it 4.077 r_mcangle_it 3.976 r_mcbond_it 2.92 r_angle_refined_deg 2.098 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.848 r_dihedral_angle_4_deg 18.224 r_dihedral_angle_3_deg 17.436 r_long_range_B_refined 7.179 r_dihedral_angle_1_deg 7.057 r_scbond_it 4.077 r_mcangle_it 3.976 r_mcbond_it 2.92 r_angle_refined_deg 2.098 r_chiral_restr 0.136 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8810 Nucleic Acid Atoms Solvent Atoms 621 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing ARP model building Coot model building