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Nicotinic acid mononucleotide (NaMN) adenylyltransferase from Bacillus anthracis: product complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KAM PDB entry 1kam
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.856 α = 90 b = 137.413 β = 90 c = 143.972 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV++ Osmic VariMax M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 98.9 0.085 0.085 15.9 43353
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1kam 2.2 50 40803 2162 99.41 0.2048 0.20117 0.2039 0.2734 RANDOM 32.75
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] 1.53 -1.95 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.763 r_dihedral_angle_4_deg 22.225 r_dihedral_angle_3_deg 19.848 r_dihedral_angle_1_deg 5.988 r_scangle_it 2.945 r_scbond_it 1.948 r_angle_refined_deg 1.561 r_mcangle_it 1.465 r_mcbond_it 0.861 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.763 r_dihedral_angle_4_deg 22.225 r_dihedral_angle_3_deg 19.848 r_dihedral_angle_1_deg 5.988 r_scangle_it 2.945 r_scbond_it 1.948 r_angle_refined_deg 1.561 r_mcangle_it 1.465 r_mcbond_it 0.861 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.201 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.113 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 6173 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing