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Crystal structure of Human NMPRTase as free-form
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 2.35 47.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.564 α = 90 b = 106.4 β = 96.5 c = 82.781 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 2006-06-02 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 97.2 0.078 15.3 1.9 70989
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 2.07 93.2 0.377 2.34 1.8 4546
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 19.94 64876 3452 97.19 0.18514 0.18337 0.1839 0.21851 0.2189 RANDOM 21.587
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 36.232 r_dihedral_angle_3_deg 11.95 r_dihedral_angle_4_deg 10.364 r_dihedral_angle_1_deg 5.046 r_scangle_it 1.244 r_angle_refined_deg 0.933 r_scbond_it 0.748 r_mcangle_it 0.578 r_mcbond_it 0.336 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.232 r_dihedral_angle_3_deg 11.95 r_dihedral_angle_4_deg 10.364 r_dihedral_angle_1_deg 5.046 r_scangle_it 1.244 r_angle_refined_deg 0.933 r_scbond_it 0.748 r_mcangle_it 0.578 r_mcbond_it 0.336 r_nbtor_refined 0.298 r_nbd_refined 0.173 r_symmetry_vdw_refined 0.141 r_symmetry_hbond_refined 0.096 r_xyhbond_nbd_refined 0.093 r_chiral_restr 0.066 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 820 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing