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Structure of apo anthocyanidin reductase from vitis vinifera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C29 PDB ENTRY 2C29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 NH4 acetate 150 mM, PEG 3350, Hepes 100 mM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.47 α = 90 b = 50.47 β = 90 c = 440.406 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 CCD ADSC QUANTUM 210 MIRRORS 2007-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.22 43.727 96.4 0.087 0.087 5.6 11.7 17253 42.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.22 2.34 98.8 0.343 0.343 2 12.2
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 2C29 2.22 30 17114 17114 851 95.7 0.203 0.199 0.2083 0.27 0.285 RANDOM 34.07
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] 0.88 0.44 0.88 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.824 r_dihedral_angle_4_deg 19.97 r_dihedral_angle_3_deg 14.543 r_scangle_it 5.915 r_dihedral_angle_1_deg 5.765 r_mcangle_it 4.565 r_scbond_it 4.303 r_mcbond_it 3.21 r_angle_refined_deg 2.068 r_angle_other_deg 1.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.824 r_dihedral_angle_4_deg 19.97 r_dihedral_angle_3_deg 14.543 r_scangle_it 5.915 r_dihedral_angle_1_deg 5.765 r_mcangle_it 4.565 r_scbond_it 4.303 r_mcbond_it 3.21 r_angle_refined_deg 2.068 r_angle_other_deg 1.229 r_mcbond_other 0.695 r_symmetry_hbond_refined 0.345 r_nbd_refined 0.21 r_nbd_other 0.184 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_other 0.175 r_chiral_restr 0.118 r_symmetry_vdw_refined 0.118 r_nbtor_other 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2309 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 1
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction