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Crystal Structure of Human Inosine Triphosphate Pyrophosphatase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CAR PDB entry 2CAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 27% PEG 3350
100mM HEPES pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 34.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.126 α = 90 b = 104.99 β = 90 c = 49.888 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV mirrors 2006-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.63 105 98.1 0.054 0.048 35.7 5.9 20838 20838 20.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.63 1.69 98.2 0.395 0.442 3.3 5.3 20838
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2CAR 1.63 29.84 19784 19784 1075 98.05 0.193 0.19 0.1874 0.24 0.2355 RANDOM 20.782
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] 0.28 -0.53 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.317 r_dihedral_angle_4_deg 18.01 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_1_deg 5.463 r_scangle_it 3.618 r_scbond_it 2.475 r_mcangle_it 1.463 r_angle_refined_deg 1.391 r_mcbond_it 0.916 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.317 r_dihedral_angle_4_deg 18.01 r_dihedral_angle_3_deg 15.08 r_dihedral_angle_1_deg 5.463 r_scangle_it 3.618 r_scbond_it 2.475 r_mcangle_it 1.463 r_angle_refined_deg 1.391 r_mcbond_it 0.916 r_nbtor_refined 0.311 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.211 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1660 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction