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Crystal structure of a nicotinate nucleotide pyrophosphorylase (tm1645) from thermotoga maritima at 2.50 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QPN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 6 293 10% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.57 65.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.371 α = 90 b = 126.125 β = 90 c = 138.372 γ = 90
Symmetry Space Group I 2 2 2
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 315 flat mirror 2002-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.501 38.29 99.2 0.081 12.6 4.3 29194 29194 63.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.57 93.2 0.546 2 3.9 2002
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 1QPN 2.5 38.29 27683 1510 98.96 0.216 0.21295 0.2116 0.27225 0.2671 RANDOM 37.427
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] 3.48 0.4 -3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.854 r_dihedral_angle_4_deg 19.228 r_dihedral_angle_3_deg 17.661 r_dihedral_angle_1_deg 6.607 r_scangle_it 3.795 r_scbond_it 2.092 r_angle_refined_deg 1.516 r_mcangle_it 1.388 r_angle_other_deg 0.835 r_mcbond_it 0.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.854 r_dihedral_angle_4_deg 19.228 r_dihedral_angle_3_deg 17.661 r_dihedral_angle_1_deg 6.607 r_scangle_it 3.795 r_scbond_it 2.092 r_angle_refined_deg 1.516 r_mcangle_it 1.388 r_angle_other_deg 0.835 r_mcbond_it 0.728 r_symmetry_vdw_other 0.296 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.182 r_nbd_other 0.178 r_nbtor_other 0.089 r_chiral_restr 0.084 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4074 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling