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Crystal structure of the carboxyltransferase domain of the oxaloacetate decarboxylase Na+ pump from Vibrio cholerae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RQH PDB ENTRY 1RQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 298 0.1 M Na-cacodylate
0.2 M (NH4)2SO4
5% glycerol
25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.35 47.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.825 α = 90 b = 91.655 β = 90 c = 116.422 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 225 mm CCD 2005-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.7 35 98.5 0.123 0.104 13.8 7.14 105661 31.19
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 1.7 35 95.5 0.578 0.809 2.47 5.82
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 1RQH 1.7 35 100388 100388 5272 98.5 0.235 0.232 0.2381 0.284 0.2876 RANDOM 21.67
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] -2.13 0.1 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.832 r_dihedral_angle_4_deg 15.997 r_dihedral_angle_3_deg 15.62 r_dihedral_angle_1_deg 5.751 r_scangle_it 5.668 r_scbond_it 4.605 r_mcangle_it 2.724 r_mcbond_it 2.084 r_angle_refined_deg 1.441 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.832 r_dihedral_angle_4_deg 15.997 r_dihedral_angle_3_deg 15.62 r_dihedral_angle_1_deg 5.751 r_scangle_it 5.668 r_scbond_it 4.605 r_mcangle_it 2.724 r_mcbond_it 2.084 r_angle_refined_deg 1.441 r_nbtor_refined 0.303 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.157 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 6994 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing