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X-ray structure of Pyrococcus horikoshii OT3 alcohol dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other An initial model was generated by PHYRE2 Server
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 200 mM potassium phosphate, 29% w/v polyethylene glycol 3350, 3 mM NAD+, 10 mM NiCl2, 2% v/v butanol, pH 4.9
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.89 α = 90 b = 75.58 β = 90 c = 166.5 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 IMAGE PLATE RIGAKU RAXIS 2017-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.94 19.5 98.2 0.99 20.3 6.8 63980
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 0.92
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE An initial model was generated by PHYRE2 Server 1.94 19.497 63980 3170 98.192 0.22 0.2184 0.2258 0.2526 0.2581 21.441
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] -0.23 -0.114 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.633 r_dihedral_angle_4_deg 21.004 r_dihedral_angle_3_deg 15.181 r_dihedral_angle_1_deg 7.168 r_lrange_it 5.395 r_lrange_other 5.26 r_scangle_it 3.593 r_scangle_other 3.592 r_scbond_it 2.742 r_scbond_other 2.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.633 r_dihedral_angle_4_deg 21.004 r_dihedral_angle_3_deg 15.181 r_dihedral_angle_1_deg 7.168 r_lrange_it 5.395 r_lrange_other 5.26 r_scangle_it 3.593 r_scangle_other 3.592 r_scbond_it 2.742 r_scbond_other 2.741 r_mcangle_other 2.243 r_mcangle_it 2.242 r_mcbond_it 1.49 r_mcbond_other 1.486 r_angle_refined_deg 1.284 r_angle_other_deg 1.253 r_symmetry_nbd_refined 0.268 r_nbd_other 0.213 r_nbd_refined 0.204 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.094 r_symmetry_xyhbond_nbd_refined 0.08 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.059 r_gen_planes_refined 0.016 r_bond_refined_d 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5836 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing