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Crystal Structure of human Pex3p in complex with N-terminal Pex19p peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 25% PEG 3350, 0.2M NaCl, 50mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.6 α = 90 b = 147.6 β = 90 c = 86.202 γ = 120
Symmetry Space Group P 65 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 90 CCD ADSC QUANTUM 315 2007-12-06 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD RIGAKU JUPITER 210 2008-02-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU 2 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9791, 0.9794, 0.9642 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 2.5 50 99.6 0.055 46.273 10.3 19774 19695 1 1
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) 2.5 2.59 99.9 0.267 10.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.5 48.34 19550 18591 1001 100 0.22095 0.21923 0.2162 0.25435 0.2476 RANDOM 50.555
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] 0.86 0.43 0.86 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.688 r_dihedral_angle_4_deg 21.595 r_dihedral_angle_3_deg 16.329 r_dihedral_angle_1_deg 5.544 r_scangle_it 3.992 r_scbond_it 2.338 r_mcangle_it 1.571 r_angle_refined_deg 1.461 r_mcbond_it 0.799 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.688 r_dihedral_angle_4_deg 21.595 r_dihedral_angle_3_deg 16.329 r_dihedral_angle_1_deg 5.544 r_scangle_it 3.992 r_scbond_it 2.338 r_mcangle_it 1.571 r_angle_refined_deg 1.461 r_mcbond_it 0.799 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2379 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing