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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 1IYZ PDB ENTRY 1IYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 0.22M LITHIUM SULPHATE, 0.1M SODIUM ACETATE PH4.0, 45% PEG300, pH 4.00
Crystal Properties Matthews coefficient Solvent content 2.28 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.86 α = 90 b = 46.86 β = 90 c = 315.93 γ = 90
Symmetry Space Group P 43 2 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 CCD MARRESEARCH 2005-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.5 30 99.8 0.1 12.1 6.58 13313 62
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 2.5 2.59 99.6 0.38 4.4 4.8
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 1IYZ 2.5 30 12550 669 99.9 0.228 0.226 0.2237 0.271 0.2639 RANDOM 53.82
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] 1.93 1.93 -3.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.032 r_dihedral_angle_4_deg 19.063 r_dihedral_angle_3_deg 15.797 r_dihedral_angle_1_deg 6.68 r_scangle_it 1.64 r_angle_refined_deg 1.302 r_scbond_it 1.063 r_angle_other_deg 0.81 r_mcangle_it 0.671 r_mcbond_it 0.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.032 r_dihedral_angle_4_deg 19.063 r_dihedral_angle_3_deg 15.797 r_dihedral_angle_1_deg 6.68 r_scangle_it 1.64 r_angle_refined_deg 1.302 r_scbond_it 1.063 r_angle_other_deg 0.81 r_mcangle_it 0.671 r_mcbond_it 0.407 r_nbd_refined 0.218 r_nbd_other 0.195 r_nbtor_refined 0.188 r_symmetry_vdw_other 0.181 r_xyhbond_nbd_refined 0.14 r_symmetry_vdw_refined 0.107 r_nbtor_other 0.089 r_chiral_restr 0.066 r_symmetry_hbond_refined 0.052 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2344 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing