☰ Navigation Tabs
Crystal Structure of Plasmodium Berghei Orotidine 5'-monophosphate Decarboxylase (ortholog of Plasmodium falciparum PF10_0225)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AQW PDB Entry: 2AQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 16% Peg3350, 140mM diammonium hydrogen citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.03 39.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.202 α = 90 b = 108.623 β = 97.3 c = 69.89 γ = 90
Symmetry Space Group P 1 21 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 2005-10-31 SINGLE WAVELENGTH 2 1 x-ray
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.72 50 94.4 0.047 3 65456
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) 1.72 1.78 67 0.382 1.9 4637
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 (All) 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: 2AQW 1.72 29.22 65422 3308 94.27 0.188 0.186 0.1835 0.221 0.2167 RANDOM 25.168
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.674 r_dihedral_angle_4_deg 17.932 r_dihedral_angle_3_deg 13.629 r_dihedral_angle_1_deg 5.715 r_mcangle_it 2.034 r_scangle_it 2.028 r_scbond_it 1.374 r_angle_refined_deg 1.314 r_mcbond_it 1.276 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.674 r_dihedral_angle_4_deg 17.932 r_dihedral_angle_3_deg 13.629 r_dihedral_angle_1_deg 5.715 r_mcangle_it 2.034 r_scangle_it 2.028 r_scbond_it 1.374 r_angle_refined_deg 1.314 r_mcbond_it 1.276 r_nbtor_refined 0.306 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.181 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.105 r_symmetry_hbond_refined 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5438 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 2
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction