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Structure of putative orotidine-monophosphate-decarboxylase from Plasmodium yoelii (PY01515)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 297 2.5 M (NH4)2SO4, Bis-Tris propane pH 7.0 and 10mM NaI, VAPOR DIFFUSION, temperature 297K
Crystal Properties Matthews coefficient Solvent content 1.9 35.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.632 α = 90 b = 61.632 β = 90 c = 274.284 γ = 120
Symmetry Space Group P 61 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 100 CCD ADSC QUANTUM 4 Si111 2005-07-23 M MAD 2 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV VeriMax 2005-08-11 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.9797 APS 17-ID 2 ROTATING ANODE RIGAKU FR-E 1.54
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 2 20 99.1 0.9 0.9 9.1 6 21954 21895 28.6
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 2 2.07 97.1 0.546 0.546 2.35 4.8 2073
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2 20 21954 21145 710 99.27 0.21217 0.21217 0.21057 0.26154 0.213 RANDOM 29.695
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] 1.53 0.77 1.53 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.264 r_dihedral_angle_4_deg 22 r_dihedral_angle_3_deg 16.224 r_dihedral_angle_1_deg 6.316 r_scangle_it 3.837 r_scbond_it 2.736 r_mcangle_it 1.678 r_angle_refined_deg 1.673 r_mcbond_it 1.086 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.264 r_dihedral_angle_4_deg 22 r_dihedral_angle_3_deg 16.224 r_dihedral_angle_1_deg 6.316 r_scangle_it 3.837 r_scbond_it 2.736 r_mcangle_it 1.678 r_angle_refined_deg 1.673 r_mcbond_it 1.086 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.271 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_refined 0.174 r_chiral_restr 0.129 r_bond_refined_d 0.023 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 2633 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling SOLVE phasing O model building