☰ Navigation Tabs
Plasmodium yoelii Ribonucleotide Reductase Subunit R2 (PY03671)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PIY PDB entry 1PIY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 2.0 M Sodium formate, 100 mM Hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.04 α = 90 b = 153.46 β = 132 c = 143.36 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 CCD ADSC QUANTUM 210 2005-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.97972 APS 17-ID
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 2.5 30 98.7 0.07 0.048 14.7 3.6 104627 104627
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 2.5 2.59 88 0.767 0.767 1.2 2.9
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 1PIY 2.7 19.99 70611 70611 3552 100 0.30692 0.3038 0.2972 0.36797 0.352 RANDOM 41.924
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] 0.42 0.29 -0.38 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.949 r_dihedral_angle_3_deg 23.316 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_1_deg 7.689 r_scangle_it 3.103 r_scbond_it 2.151 r_angle_refined_deg 2.004 r_mcangle_it 1.164 r_mcbond_it 0.634 r_symmetry_vdw_refined 0.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.949 r_dihedral_angle_3_deg 23.316 r_dihedral_angle_4_deg 19.077 r_dihedral_angle_1_deg 7.689 r_scangle_it 3.103 r_scbond_it 2.151 r_angle_refined_deg 2.004 r_mcangle_it 1.164 r_mcbond_it 0.634 r_symmetry_vdw_refined 0.508 r_symmetry_hbond_refined 0.451 r_nbtor_refined 0.328 r_nbd_refined 0.292 r_xyhbond_nbd_refined 0.244 r_chiral_restr 0.141 r_bond_refined_d 0.022 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 16775 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling PHASER phasing