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Crystal Structure of the Y82F variant of ECH2 decarboxylase domain of CurF from Lyngbya majuscula
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q34 PDB ENTRY 2Q34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.15 277.15 1.5M sodium malonate pH 7.0, 50 mM HEPES pH 6.8, 20 mM Tris pH 7.9, 500 mM NaCl, 10% glycerol, pH 7.15, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.138 α = 90 b = 106.138 β = 90 c = 119.497 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 100 CCD MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2006-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 1.65 50 99.9 0.061 12.6 10.9 31133 31133 1 1 23.6
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 1.65 1.71 100 0.609 3.7 9.6 3069
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 2Q34 1.65 33.36 31133 31124 1571 99.7 0.169 0.167 0.191 0.204 0.214 RANDOM 21.465
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] -1.64 -0.82 -1.64 2.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.188 r_dihedral_angle_4_deg 19.237 r_dihedral_angle_3_deg 14.076 r_scangle_it 5.966 r_dihedral_angle_1_deg 4.941 r_scbond_it 3.878 r_mcangle_it 1.761 r_angle_refined_deg 1.316 r_mcbond_it 1.206 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.188 r_dihedral_angle_4_deg 19.237 r_dihedral_angle_3_deg 14.076 r_scangle_it 5.966 r_dihedral_angle_1_deg 4.941 r_scbond_it 3.878 r_mcangle_it 1.761 r_angle_refined_deg 1.316 r_mcbond_it 1.206 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.268 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1894 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction PHASER phasing