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Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XD3 PDB ENTRY 1XD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 100 MM BIS-TRIS PH 5.5, 200 MM NACL, 25 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.3 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.4 α = 90 b = 75.3 β = 90 c = 85.7 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 CCD ADSC CCD TRIPLE STRIPED VERTICAL AND HORIZANTAL FOCUSSING MIRRORS IN KIRKPATRICK- BAEZ GEOMETRY 2007-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C APS 24-ID-C
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 2.3 30 98.1 0.11 8 5.7 39592 3
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 2.3 2.36 90.2 0.45 2.1 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1XD3 2.3 19.85 38252 1062 100 0.188 0.187 0.235 0.259 RANDOM 35.33
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] -0.8 3.3 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.591 r_dihedral_angle_4_deg 22.751 r_dihedral_angle_3_deg 17.4 r_dihedral_angle_1_deg 5.939 r_scangle_it 3.121 r_scbond_it 1.932 r_mcangle_it 1.354 r_angle_refined_deg 1.319 r_angle_other_deg 0.908 r_mcbond_it 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.591 r_dihedral_angle_4_deg 22.751 r_dihedral_angle_3_deg 17.4 r_dihedral_angle_1_deg 5.939 r_scangle_it 3.121 r_scbond_it 1.932 r_mcangle_it 1.354 r_angle_refined_deg 1.319 r_angle_other_deg 0.908 r_mcbond_it 0.71 r_chiral_restr 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_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 4564 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing