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Crystal structure of human 4-Hydroxyphenylpyruvate dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SQI PDB ENTRY 1SQI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2M SODIUM ACETATE, 0.1M BIS-TRIS PROPANE PH 6.5, 20% PEG 3350, 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.77 55.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.206 α = 90 b = 99.206 β = 90 c = 87.726 γ = 120
Symmetry Space Group P 31 2 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 RAYONIX MX-300 2009-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9778 Diamond I24
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 1.75 61.38 100 0.11 0.066 8.4 3.7 50642 50630 2 2
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 1.75 1.84 99.9 0.776 0.464 2.2 3.7 7291
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 (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 1SQI 1.75 49.6 48102 48037 2572 99.96 0.14511 0.14362 0.1573 0.17385 0.1887 RANDOM 11.085
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] 0.32 0.16 0.32 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.502 r_dihedral_angle_4_deg 17.525 r_dihedral_angle_3_deg 12.182 r_dihedral_angle_1_deg 6.309 r_scangle_it 4.454 r_scbond_it 2.693 r_mcangle_it 1.534 r_angle_refined_deg 1.475 r_angle_other_deg 0.889 r_mcbond_it 0.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.502 r_dihedral_angle_4_deg 17.525 r_dihedral_angle_3_deg 12.182 r_dihedral_angle_1_deg 6.309 r_scangle_it 4.454 r_scbond_it 2.693 r_mcangle_it 1.534 r_angle_refined_deg 1.475 r_angle_other_deg 0.889 r_mcbond_it 0.848 r_mcbond_other 0.275 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3033 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 19
Software Software Software Name Purpose PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling