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NADH bound to the dehydrogenase domain of the bifunctional mannitol-1-phosphate dehydrogenase/phosphatase MtlD from Acinetobacter baumannii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1M BIS-Tris propane pH6.5, 0.25M Na2SO4, 16% PEG3350, 0.02M MgCl2, 0.1M KI with microseeding
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.301 α = 90 b = 157.337 β = 90 c = 219.02 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 9M 2018-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98 SOLEIL PROXIMA 2
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 2.9 48.42 100 0.153 0.158 0.042 0.999 13.4 13.9 38418
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 2.9 3.03 100 1.836 1.905 0.506 0.796 14
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 7OCN 2.9 48.42 36499 1881 99.97 0.235 0.2324 0.2311 0.2884 0.2818 RANDOM 94.288
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] -3.46 -5.92 9.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.131 r_dihedral_angle_3_deg 12.753 r_dihedral_angle_4_deg 11.478 r_dihedral_angle_1_deg 4.83 r_angle_refined_deg 1.145 r_angle_other_deg 1.021 r_chiral_restr 0.03 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.131 r_dihedral_angle_3_deg 12.753 r_dihedral_angle_4_deg 11.478 r_dihedral_angle_1_deg 4.83 r_angle_refined_deg 1.145 r_angle_other_deg 1.021 r_chiral_restr 0.03 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11019 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction REFMAC phasing