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ANTHOCYANIDIN SYNTHASE FROM ARABIDOPSIS THALIANA COMPLEXED with naringenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GP4 PDB ENTRY 1GP4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 18% (W/V) PEG 2000 MONOMETHYLETHER, 50MM MES, 200MM AMMONIUM ACETATE, 2MM FESO4, 10MM POTASSIUM ALPHA-KETOGLUTARATE, 10MM SODIUM ASCORBATE, 2.5MM RACEMIC NARINGENIN IN 10% (V/V) MEOH, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.33 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.807 α = 90 b = 62.309 β = 90 c = 102.493 γ = 90
Symmetry Space Group P 21 21 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 ADSC CCD MIRROR 2001-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 2.2 40 98 0.08 15.8 5.9 18607 42.5
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 2.31 99.5 0.61 3.1 5.6
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 PDB ENTRY 1GP4 2.2 53.22 17793 785 97 0.211 0.208 0.2158 0.268 0.2689 RANDOM 43.42
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] -0.54 2.31 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.807 r_dihedral_angle_3_deg 16.659 r_dihedral_angle_4_deg 15.978 r_dihedral_angle_1_deg 7.457 r_scangle_it 3.245 r_scbond_it 2.24 r_angle_refined_deg 1.887 r_mcangle_it 1.316 r_angle_other_deg 0.913 r_mcbond_it 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.807 r_dihedral_angle_3_deg 16.659 r_dihedral_angle_4_deg 15.978 r_dihedral_angle_1_deg 7.457 r_scangle_it 3.245 r_scbond_it 2.24 r_angle_refined_deg 1.887 r_mcangle_it 1.316 r_angle_other_deg 0.913 r_mcbond_it 0.85 r_symmetry_vdw_refined 0.314 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.194 r_nbd_other 0.193 r_nbtor_refined 0.185 r_symmetry_vdw_other 0.183 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.103 r_nbtor_other 0.09 r_bond_refined_d 0.025 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 2685 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing