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Levoglucosan dehydrogenase, apo form
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 6.5 293 sodium cacodylate, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.2 44.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.649 α = 90 b = 95.649 β = 90 c = 170.912 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 2M-F 2015-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
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 1.8 50 99.9 0.093 35.4 14.2 74076
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 1.8 1.83 100 0.694 0.974 3.4 13.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4H3V 1.8 38.28 70139 3758 99.75 0.16839 0.16657 0.20192 0.1953 RANDOM 27.844
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.417 r_dihedral_angle_4_deg 16.715 r_dihedral_angle_3_deg 12.565 r_dihedral_angle_1_deg 7.267 r_long_range_B_refined 5.27 r_long_range_B_other 5.187 r_scangle_other 4.3 r_mcangle_other 3.175 r_mcangle_it 3.173 r_scbond_it 3.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.417 r_dihedral_angle_4_deg 16.715 r_dihedral_angle_3_deg 12.565 r_dihedral_angle_1_deg 7.267 r_long_range_B_refined 5.27 r_long_range_B_other 5.187 r_scangle_other 4.3 r_mcangle_other 3.175 r_mcangle_it 3.173 r_scbond_it 3.019 r_scbond_other 2.958 r_mcbond_it 2.332 r_mcbond_other 2.332 r_angle_refined_deg 1.555 r_angle_other_deg 0.529 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 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 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 5851 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing