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Pseudomonas aeruginosa nicotinamide adenine dinucleotide kinase (NADK) structure in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AN1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.1 mM Tris pH 8.5, 0.8 mM AmSO4
Crystal Properties Matthews coefficient Solvent content 2.58 52.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.77 α = 90 b = 88.77 β = 90 c = 174.247 γ = 90
Symmetry Space Group P 41 2 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 2019-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 79.097 100 1 39.2 20 31752 31.47
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 2.3 2.34 99.7 0.656 0.669 0.131 1 5.4 15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2AN1 2.3 29.59 1.34 31706 1570 99.82 0.1989 0.197 0.1969 0.2358 0.2371 RANDOM 41.74
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.3747 f_angle_d 1.5165 f_chiral_restr 0.2127 f_bond_d 0.0128 f_plane_restr 0.0127
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4247 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing