☰ Navigation Tabs
Crystal structure of the plant stress-response enzyme AKR4C8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H7U PDB entry 3H7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 200 mM Ammonium acetate, 50 mM Tri-sodium citrate dihydrate pH 6.0, 5% v/v Ethylene glycol, 32% w/v PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.34 47.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.431 α = 90 b = 39.909 β = 99.63 c = 47.223 γ = 90
Symmetry Space Group C 1 2 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 MAR CCD 165 mm 2004-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.4 29.24 99.1 0.069 0.069 13.5 4 63103 62514 14.1
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) 1.4 1.48 99.9 0.395 3.4 4 9158
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 3H7U 1.4 28.24 59308 3201 99.06 0.15646 0.15505 0.1587 0.18303 0.1812 RANDOM 14.198
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] -0.03 -0.19 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.702 r_dihedral_angle_3_deg 11.4 r_dihedral_angle_4_deg 8.151 r_dihedral_angle_1_deg 5.12 r_scangle_it 2.886 r_scbond_it 1.821 r_angle_refined_deg 1.434 r_mcangle_it 1.108 r_angle_other_deg 0.865 r_mcbond_it 0.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.702 r_dihedral_angle_3_deg 11.4 r_dihedral_angle_4_deg 8.151 r_dihedral_angle_1_deg 5.12 r_scangle_it 2.886 r_scbond_it 1.821 r_angle_refined_deg 1.434 r_mcangle_it 1.108 r_angle_other_deg 0.865 r_mcbond_it 0.611 r_mcbond_other 0.168 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2585 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 106
Software Software Software Name Purpose MAR345 data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling