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Structure of potato (Solanum tuberosum) epoxide hydrolase I (StEH1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJ5 PDB ENTRY 1VJ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% PEG 10, 000), AND EQUILIBRATED BY SITTING-DROP VAPOR DIFFUSION AT ROOM TEMPERATURE.
Crystal Properties Matthews coefficient Solvent content 2.2 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.926 α = 90 b = 98.532 β = 90 c = 122.033 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 2004-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.95 31.6 99.2 0.06 20.9 5.1 49514 30.41
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 1.95 2.06 98.6 0.47 3.1 5
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 1VJ5 1.95 31.6 47002 2510 99 0.205 0.203 0.2035 0.24 0.243 RANDOM 32.8
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] -1.26 2.73 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.025 r_dihedral_angle_4_deg 17.744 r_dihedral_angle_3_deg 12.822 r_dihedral_angle_1_deg 5.248 r_scangle_it 1.512 r_angle_refined_deg 1.064 r_scbond_it 0.957 r_mcangle_it 0.823 r_mcbond_it 0.475 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.025 r_dihedral_angle_4_deg 17.744 r_dihedral_angle_3_deg 12.822 r_dihedral_angle_1_deg 5.248 r_scangle_it 1.512 r_angle_refined_deg 1.064 r_scbond_it 0.957 r_mcangle_it 0.823 r_mcbond_it 0.475 r_nbtor_refined 0.303 r_nbd_refined 0.179 r_symmetry_vdw_refined 0.144 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.104 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 5115 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing