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Structure of NMN synthetase from Francisella tularensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KQP PDB ENTRY 1kqp
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M K/Na tartrate, 16% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.432 α = 90 b = 126.438 β = 90 c = 152.531 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 100 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 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 1.85 50 94 0.044 79468
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 PDB ENTRY 1kqp 1.85 40 75114 3935 93.86 0.18662 0.18411 0.23338 0.2344 RANDOM 26.216
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] 0.35 0.18 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.516 r_dihedral_angle_4_deg 19.147 r_dihedral_angle_3_deg 14.863 r_scangle_it 5.884 r_dihedral_angle_1_deg 5.61 r_scbond_it 3.78 r_mcangle_it 2.316 r_angle_refined_deg 1.391 r_mcbond_it 1.384 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.516 r_dihedral_angle_4_deg 19.147 r_dihedral_angle_3_deg 14.863 r_scangle_it 5.884 r_dihedral_angle_1_deg 5.61 r_scbond_it 3.78 r_mcangle_it 2.316 r_angle_refined_deg 1.391 r_mcbond_it 1.384 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.262 r_symmetry_hbond_refined 0.217 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.096 r_metal_ion_refined 0.043 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_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 7564 Nucleic Acid Atoms Solvent Atoms 812 Heterogen Atoms 140
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling