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Crystal Structure of Plasmodium falciparum Ubiquitin Carboxyl- terminal Hydrolase 3 (UCHL3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WDT PDB ENTRY 2WDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 100 MM BICINE PH 9.0, 300 MM MGCL2, 25% PEG 2000, 15% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.2 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.343 α = 90 b = 44.979 β = 121.79 c = 99.534 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC MIRRORS 2007-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 2.42 30 99.2 0.08 11.1 2.9 24494 2
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 2.42 2.46 96.2 0.49 2.3 2.7
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 2WDT 2.42 28.21 23466 1024 99 0.219 0.218 0.2189 0.251 0.2497 RANDOM 35.98
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 0.25 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.214 r_dihedral_angle_3_deg 17.7 r_dihedral_angle_4_deg 13.989 r_dihedral_angle_1_deg 6.028 r_scangle_it 1.84 r_angle_refined_deg 1.28 r_scbond_it 1.181 r_angle_other_deg 0.872 r_mcangle_it 0.744 r_mcbond_it 0.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.214 r_dihedral_angle_3_deg 17.7 r_dihedral_angle_4_deg 13.989 r_dihedral_angle_1_deg 6.028 r_scangle_it 1.84 r_angle_refined_deg 1.28 r_scbond_it 1.181 r_angle_other_deg 0.872 r_mcangle_it 0.744 r_mcbond_it 0.404 r_chiral_restr 0.077 r_bond_refined_d 0.011 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 3394 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing