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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 2RH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.85 293 0.12 M MGCL2, 0.1 M BIS6TRIS PH 6.85, 21% PEG 3350, 2.5 % GLYCEROL, TEMERATURE 293K, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal Properties Matthews coefficient Solvent content 2.37 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.518 α = 90 b = 51.012 β = 110.31 c = 86.113 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 210 mirrors 2008-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 3.17 80.84 99.8 0.089 6 3.3 11952 11952
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.17 3.34 99.9 0.389 2 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT 2rh8 3.17 79.31 11368 576 99.74 0.22518 0.22141 0.29912 0.2736 RANDOM 37.397
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] -2.39 0.9 0.59 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.444 r_dihedral_angle_3_deg 20.921 r_dihedral_angle_4_deg 16.631 r_dihedral_angle_1_deg 6.254 r_angle_other_deg 4.642 r_scangle_it 1.408 r_angle_refined_deg 1.309 r_mcangle_it 0.893 r_scbond_it 0.79 r_mcbond_it 0.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.444 r_dihedral_angle_3_deg 20.921 r_dihedral_angle_4_deg 16.631 r_dihedral_angle_1_deg 6.254 r_angle_other_deg 4.642 r_scangle_it 1.408 r_angle_refined_deg 1.309 r_mcangle_it 0.893 r_scbond_it 0.79 r_mcbond_it 0.479 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4286 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling