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Crystal structure of Herbaspirillum huttiense L-arabinose 1-dehydrogenase (NAD bound form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NUG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Sodium formate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.509 α = 90 b = 83.562 β = 113.04 c = 81.927 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 PIXEL DECTRIS PILATUS 6M 2021-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.36 42.82 99.8 0.236 0.249 0.079 0.993 8.3 9.9 114656
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.38 97.9 2.032 2.154 0.701 0.576 9.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NUG 1.36 42.82 108813 5835 99.84 0.1691 0.1678 0.1679 0.1922 0.192 RANDOM 12.04
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] 1.14 -0.3 0.05 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.85 r_dihedral_angle_3_deg 13.032 r_dihedral_angle_4_deg 11.478 r_dihedral_angle_1_deg 6.654 r_angle_refined_deg 1.807 r_angle_other_deg 1.608 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.85 r_dihedral_angle_3_deg 13.032 r_dihedral_angle_4_deg 11.478 r_dihedral_angle_1_deg 6.654 r_angle_refined_deg 1.807 r_angle_other_deg 1.608 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3866 Nucleic Acid Atoms Solvent Atoms 550 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement XDS data scaling PDB_EXTRACT data extraction BALBES phasing