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Crystal structure of LmNADK1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I2B PDB ENTRY 2i2b
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.481 α = 90 b = 75.851 β = 90 c = 118.35 γ = 90
Symmetry Space Group I 2 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 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.933 ESRF ID23-1
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 2.22 37.9 96.8 0.054 22.9 4.9 13780 13383 38.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.34 81.2 0.411 3.5 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 2i2b 2.22 37.93 13780 13383 405 96.57 0.208 0.208 0.207 0.252 0.2541 RANDOM 34.883
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] 0.68 1.85 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.036 r_dihedral_angle_4_deg 15.371 r_dihedral_angle_3_deg 15.103 r_dihedral_angle_1_deg 9.347 r_angle_refined_deg 2.257 r_scangle_it 1.502 r_scbond_it 1.116 r_angle_other_deg 0.958 r_mcangle_it 0.778 r_mcbond_it 0.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.036 r_dihedral_angle_4_deg 15.371 r_dihedral_angle_3_deg 15.103 r_dihedral_angle_1_deg 9.347 r_angle_refined_deg 2.257 r_scangle_it 1.502 r_scbond_it 1.116 r_angle_other_deg 0.958 r_mcangle_it 0.778 r_mcbond_it 0.472 r_chiral_restr 0.339 r_symmetry_hbond_refined 0.335 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.293 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.194 r_nbtor_other 0.116 r_nbd_other 0.063 r_bond_refined_d 0.012 r_bond_other_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1979 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing