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Levoglucosan dehydrogenase, complex with NADH and levoglucosan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 MES-NaOH, PEG 3000, PEG 200, NADH, levoglucosan
Crystal Properties Matthews coefficient Solvent content 1.95 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.725 α = 90 b = 92.354 β = 104.48 c = 100.563 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 4M 2016-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.000 Photon Factory BL-1A
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 2.4 50 99.5 0.083 16.1 3.3 51934
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 99.7 0.52 0.959 2.4 3.4
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 4H3V 2.41 34.84 49298 2618 98.55 0.21861 0.21452 0.2175 0.29705 0.3014 RANDOM 63.786
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] 0.02 0.01 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.619 r_dihedral_angle_3_deg 18.569 r_dihedral_angle_4_deg 16.446 r_long_range_B_refined 8.459 r_long_range_B_other 8.459 r_dihedral_angle_1_deg 7.683 r_mcangle_it 6.479 r_mcangle_other 6.478 r_scangle_other 5.818 r_mcbond_it 4.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.619 r_dihedral_angle_3_deg 18.569 r_dihedral_angle_4_deg 16.446 r_long_range_B_refined 8.459 r_long_range_B_other 8.459 r_dihedral_angle_1_deg 7.683 r_mcangle_it 6.479 r_mcangle_other 6.478 r_scangle_other 5.818 r_mcbond_it 4.44 r_mcbond_other 4.44 r_scbond_it 3.956 r_scbond_other 3.949 r_angle_refined_deg 1.248 r_angle_other_deg 0.816 r_chiral_restr 0.057 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11366 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing