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Crystal structure of Human NMPRTase complexed with 5'-phosphoribosyl-1'-pyrophosphate
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 2.34 47.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.23 α = 90 b = 106.746 β = 96.24 c = 82.613 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 2.15 50 99.7 0.16 14.3 1.92 56429
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 2.15 2.28 98.6 0.318 2.73 1.8 4604
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 2.2 19.9 49967 2656 99.92 0.17659 0.17419 0.1755 0.22122 0.2217 RANDOM 23.969
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.028 r_dihedral_angle_4_deg 14.322 r_dihedral_angle_3_deg 12.396 r_dihedral_angle_1_deg 5.148 r_scangle_it 1.287 r_angle_refined_deg 1.007 r_scbond_it 0.766 r_mcangle_it 0.564 r_mcbond_it 0.321 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.028 r_dihedral_angle_4_deg 14.322 r_dihedral_angle_3_deg 12.396 r_dihedral_angle_1_deg 5.148 r_scangle_it 1.287 r_angle_refined_deg 1.007 r_scbond_it 0.766 r_mcangle_it 0.564 r_mcbond_it 0.321 r_nbtor_refined 0.297 r_nbd_refined 0.173 r_symmetry_vdw_refined 0.132 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.067 r_symmetry_hbond_refined 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 782 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing