☰ Navigation Tabs
Nerol dehydrogenase from Persicaria minor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 HEPES sodium, propanol, PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.2 44.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83 α = 90 b = 54.03 β = 90 c = 79.37 γ = 90
Symmetry Space Group P 21 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 6M-F 2012-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.54 79.37 96.6 0.043 0.054 0.999 13.03 2.357 52988 -3 25.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.58 96.8 0.595 0.76 0.611 1.7 2.369
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 1yqd 1.54 79.37 50260 2691 98.82 0.1504 0.1484 0.1624 0.1881 0.1952 RANDOM 22.32
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] -0.91 -0.86 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_4_deg 15.835 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_1_deg 6.21 r_angle_refined_deg 2.082 r_angle_other_deg 0.963 r_chiral_restr 0.133 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_4_deg 15.835 r_dihedral_angle_3_deg 14.438 r_dihedral_angle_1_deg 6.21 r_angle_refined_deg 2.082 r_angle_other_deg 0.963 r_chiral_restr 0.133 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2785 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 18
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction MOLREP phasing