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Crystal structure of Methanobacterium thermoautotrophicum NMNAT in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 ammonium sulfate, glycerol, TRIS, NADP
Crystal Properties Matthews coefficient Solvent content 4.07 69.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.586 α = 90 b = 124.586 β = 90 c = 111.959 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 4 2000-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0000 APS 14-BM-C
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 2.21 20 89.3 0.052 15.68 1.27 45535
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 2.21 2.31 87 0.255 4.84 1.15
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 1EJ2 2.21 20 43177 2356 89.37 0.1814 0.1806 0.1887 0.1955 0.2014 RANDOM 37.612
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] -0.45 -0.23 -0.45 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.583 r_dihedral_angle_4_deg 16.372 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 5.533 r_mcangle_it 3.378 r_mcbond_it 2.409 r_mcbond_other 2.409 r_angle_refined_deg 1.586 r_angle_other_deg 1.341 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.583 r_dihedral_angle_4_deg 16.372 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 5.533 r_mcangle_it 3.378 r_mcbond_it 2.409 r_mcbond_other 2.409 r_angle_refined_deg 1.586 r_angle_other_deg 1.341 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4033 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling AMoRE phasing