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Crystal Structure of (R)-oxirane-2-carboxylate inhibited cis-CaaD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MF8 PDB entry 3MF8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 4.6 298 three micro liter of 15.6mg/mL cis-CaaD protein sample mixed with three micro liter crystallization solution: 0.125 M CaCl2, 0.07 M sodium acetate buffer, 12.5% isopropanol, hanging drop, temperature 298K, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.26 45.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.783 α = 90 b = 96.783 β = 90 c = 96.783 γ = 90
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 2005-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 1.62 50 98.9 0.063 24 4.6 19123
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) 1.62 1.68 91.2 0.241 4.4 1751
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 (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 3MF8 1.65 50 17952 935 98.19 0.188 0.186 0.1893 0.222 0.2205 RANDOM 9.866
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 r_dihedral_angle_2_deg 38.679 r_dihedral_angle_4_deg 19.029 r_dihedral_angle_3_deg 14.534 r_dihedral_angle_1_deg 5.288 r_scangle_it 3.38 r_scbond_it 2.281 r_angle_refined_deg 1.289 r_mcangle_it 1.282 r_mcbond_it 0.864 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.679 r_dihedral_angle_4_deg 19.029 r_dihedral_angle_3_deg 14.534 r_dihedral_angle_1_deg 5.288 r_scangle_it 3.38 r_scbond_it 2.281 r_angle_refined_deg 1.289 r_mcangle_it 1.282 r_mcbond_it 0.864 r_nbtor_refined 0.306 r_nbd_refined 0.27 r_symmetry_vdw_refined 0.204 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 923 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction CaspR phasing