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1.77 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 295 7mg/mL protein, The PACT Suite condition #34 (C10), 1:1 v/v ratio, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 38.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.3 α = 90 b = 94.675 β = 90 c = 99.183 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD BE LENSES/DIAMOND LAUE MONO 2009-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G APS 21-ID-G
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 1.77 30 99.7 0.064 23.15 7 43787 -3
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) 1.77 1.8 99.3 0.565 2.77 5.4
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 1L2U 1.77 30 41524 41524 2205 99.4 0.155 0.154 0.1896 0.185 0.2174 RANDOM 29.095
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] 2.82 -0.43 -2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.78 r_dihedral_angle_4_deg 10.69 r_dihedral_angle_3_deg 10.316 r_scangle_it 3.612 r_dihedral_angle_1_deg 3.529 r_scbond_it 2.12 r_angle_refined_deg 1.383 r_mcangle_it 1.273 r_angle_other_deg 0.858 r_mcbond_it 0.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.78 r_dihedral_angle_4_deg 10.69 r_dihedral_angle_3_deg 10.316 r_scangle_it 3.612 r_dihedral_angle_1_deg 3.529 r_scbond_it 2.12 r_angle_refined_deg 1.383 r_mcangle_it 1.273 r_angle_other_deg 0.858 r_mcbond_it 0.719 r_mcbond_other 0.223 r_chiral_restr 0.084 r_bond_refined_d 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3637 Nucleic Acid Atoms Solvent Atoms 603 Heterogen Atoms 5
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling