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crystal structure of a bifunctional NMN adenylyltransferase/ADP ribose pyrophosphatase (NadM) complexed with ADPRP and NAD from Synechocystis sp.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100mM Tris, 1.5 M Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.97 75.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.54 α = 90 b = 201.54 β = 90 c = 98.695 γ = 120
Symmetry Space Group P 32 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 113 CCD 2006-04-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97874, 0.97891, 0.984 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 50 98.6 0.063 70016 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.6 43.48 66426 3549 98.51 0.19568 0.19395 0.1924 0.22774 0.2247 RANDOM 49.906
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.59 r_dihedral_angle_4_deg 22.699 r_dihedral_angle_3_deg 17.696 r_dihedral_angle_1_deg 8.649 r_scangle_it 3.256 r_scbond_it 2.019 r_angle_refined_deg 1.571 r_mcangle_it 1.551 r_mcbond_it 0.823 r_symmetry_hbond_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.59 r_dihedral_angle_4_deg 22.699 r_dihedral_angle_3_deg 17.696 r_dihedral_angle_1_deg 8.649 r_scangle_it 3.256 r_scbond_it 2.019 r_angle_refined_deg 1.571 r_mcangle_it 1.551 r_mcbond_it 0.823 r_symmetry_hbond_refined 0.331 r_nbtor_refined 0.316 r_nbd_refined 0.228 r_chiral_restr 0.162 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.156 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8022 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 287
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-2000 data reduction HKL-2000 data scaling SHELXCD phasing SHELXE model building