☰ Navigation Tabs
Crystal structure of Human NMPRTase complexed with nicotinamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H3B PDB ENTRY 2H3B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 38-40% pentaerythritol propoxylate (5/4 PO/OH), 50mM Tris-HCl, 200mM KCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.33 47.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.332 α = 90 b = 106.227 β = 96.27 c = 82.475 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU JUPITER 210 2006-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 50 98.7 0.13 13.4 1.93 71647
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 2.09 95.8 0.301 2.78 1.8 4513
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 PDB ENTRY 2H3B 2 19.99 65474 3459 98.91 0.18029 0.17875 0.179 0.20905 0.2103 RANDOM 20.214
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.561 r_dihedral_angle_4_deg 14.509 r_dihedral_angle_3_deg 12.222 r_dihedral_angle_1_deg 5.097 r_scangle_it 1.164 r_angle_refined_deg 0.939 r_scbond_it 0.707 r_mcangle_it 0.524 r_mcbond_it 0.3 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.561 r_dihedral_angle_4_deg 14.509 r_dihedral_angle_3_deg 12.222 r_dihedral_angle_1_deg 5.097 r_scangle_it 1.164 r_angle_refined_deg 0.939 r_scbond_it 0.707 r_mcangle_it 0.524 r_mcbond_it 0.3 r_nbtor_refined 0.297 r_nbd_refined 0.174 r_symmetry_vdw_refined 0.137 r_symmetry_hbond_refined 0.106 r_xyhbond_nbd_refined 0.085 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 7460 Nucleic Acid Atoms Solvent Atoms 801 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing