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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
Crystal Properties Matthews coefficient Solvent content 4.06 69.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.448 α = 90 b = 124.448 β = 90 c = 111.943 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 2.3 14.99 93.1 0.06 18.8 1.56 41867
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 2.3 2.4 93.3 0.217 6.09 1.58
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EJ2 2.3 20 39652 2202 93.16 0.1909 0.19 0.2083 0.2169 RANDOM 26.88
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] -0.62 -0.31 -0.62 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.93 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 14.175 r_dihedral_angle_1_deg 5.458 r_mcangle_it 2.415 r_mcbond_it 1.632 r_mcbond_other 1.632 r_angle_refined_deg 1.566 r_angle_other_deg 1.359 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.93 r_dihedral_angle_4_deg 17.972 r_dihedral_angle_3_deg 14.175 r_dihedral_angle_1_deg 5.458 r_mcangle_it 2.415 r_mcbond_it 1.632 r_mcbond_other 1.632 r_angle_refined_deg 1.566 r_angle_other_deg 1.359 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4000 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling AMoRE phasing