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Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 23% PEG 3000, pH 9.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.812 α = 90 b = 201.812 β = 90 c = 44.026 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 225 mm CCD 2005-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.977 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 50 99.6 4 3.2 18313
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3N3M 2.7 39.318 1.98 18309 1823 99.58 0.2004 0.1949 0.1955 0.2509 0.2504 52.5285
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.404 f_angle_d 0.971 f_chiral_restr 0.055 f_bond_d 0.008 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4979 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing