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Crystal structure of Human P53 inducible oxidoreductase (TP53I3,PIG3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J8Z PDB ENTRY 2J8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 30 % PEG 4000, 0.1 M Tris, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.78 55.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.354 α = 90 b = 184.359 β = 90 c = 318.047 γ = 90
Symmetry Space Group C 2 2 21
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 MAR scanner 300 mm plate Mirrors 2005-06-10 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) 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 3 19.94 88.7 36209 36209 45.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.2 62.5
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-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 2J8Z 3 19.94 34254 34254 1795 88.63 0.22155 0.22155 0.21955 0.2241 0.25968 0.2591 RANDOM 40.61
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] 0.65 0.57 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.838 r_dihedral_angle_3_deg 13.798 r_dihedral_angle_4_deg 12.741 r_dihedral_angle_1_deg 5.169 r_angle_refined_deg 0.935 r_angle_other_deg 0.783 r_scangle_it 0.251 r_nbd_refined 0.183 r_nbtor_refined 0.166 r_scbond_it 0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.838 r_dihedral_angle_3_deg 13.798 r_dihedral_angle_4_deg 12.741 r_dihedral_angle_1_deg 5.169 r_angle_refined_deg 0.935 r_angle_other_deg 0.783 r_scangle_it 0.251 r_nbd_refined 0.183 r_nbtor_refined 0.166 r_scbond_it 0.164 r_nbd_other 0.162 r_symmetry_vdw_other 0.152 r_symmetry_hbond_refined 0.144 r_symmetry_vdw_refined 0.143 r_xyhbond_nbd_refined 0.119 r_mcangle_it 0.091 r_nbtor_other 0.08 r_mcbond_it 0.069 r_chiral_restr 0.049 r_mcbond_other 0.016 r_bond_refined_d 0.005 r_bond_other_d 0.004 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12580 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing