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D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 8mg/mL protein, 25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.921 α = 90 b = 144.104 β = 121.44 c = 80.073 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 mirrors 2003-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
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 1.77 94.07 99.5 0.06 0.06 19.5 3.8 136908 136908 18.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 98.5 0.61 0.61 2.1 3.7 6758
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1Y9A 1.77 50 0.61 135908 135908 6880 99.95 0.14962 0.14962 0.14812 0.17793 0.1964 RANDOM 28.045
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] 1.59 0.95 -0.16 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.658 r_dihedral_angle_4_deg 14.199 r_dihedral_angle_3_deg 13.118 r_dihedral_angle_1_deg 6.176 r_scangle_it 5.946 r_scbond_it 3.943 r_mcangle_it 2.449 r_mcbond_it 1.677 r_angle_refined_deg 1.41 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.658 r_dihedral_angle_4_deg 14.199 r_dihedral_angle_3_deg 13.118 r_dihedral_angle_1_deg 6.176 r_scangle_it 5.946 r_scbond_it 3.943 r_mcangle_it 2.449 r_mcbond_it 1.677 r_angle_refined_deg 1.41 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.201 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.165 r_metal_ion_refined 0.109 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_other r_symmetry_vdw_other 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 10816 Nucleic Acid Atoms Solvent Atoms 1075 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement ProDC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing