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Crystal structure of the plant stress-response enzyme AKR4C9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S1P PDB entry 1S1P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 291 400 mM Ammonium acetate, 100 mM Tri-sodium citrate dihydrate, 37.5% w/v PEG 4000, pH 6.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.355 α = 90 b = 70.687 β = 107.22 c = 65.767 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 ADSC QUANTUM 4 2002-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 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 1.25 23.48 92 0.043 16.1 3.9 95766 87990 11.7
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 1S1P 1.25 23.48 83557 4430 91.9 0.13245 0.13121 0.1534 0.15619 0.172 RANDOM 12.05
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] 0.01 -0.04 -0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.634 r_dihedral_angle_3_deg 11.131 r_dihedral_angle_4_deg 6.678 r_dihedral_angle_1_deg 5.708 r_sphericity_free 5.298 r_scangle_it 3.347 r_sphericity_bonded 2.423 r_scbond_it 2.281 r_mcangle_it 1.618 r_angle_refined_deg 1.457
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.634 r_dihedral_angle_3_deg 11.131 r_dihedral_angle_4_deg 6.678 r_dihedral_angle_1_deg 5.708 r_sphericity_free 5.298 r_scangle_it 3.347 r_sphericity_bonded 2.423 r_scbond_it 2.281 r_mcangle_it 1.618 r_angle_refined_deg 1.457 r_rigid_bond_restr 1.025 r_mcbond_it 1.024 r_angle_other_deg 0.888 r_mcbond_other 0.454 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2511 Nucleic Acid Atoms Solvent Atoms 530 Heterogen Atoms 52
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling