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Crystal structure of Enterobacter sp. Px6-4 Ferulic Acid Decarboxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GC9 PDB ENTRY 2GC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1M HEPES pH 7.5, 20%(w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.477 α = 90 b = 88.715 β = 102.25 c = 49.264 γ = 90
Symmetry Space Group P 1 21 1
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 MAR scanner 345 mm plate 2008-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.0000
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 2.4 50 99 12722 12090
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 2GC9 2.4 36.87 12090 625 93.16 0.16668 0.16198 0.1682 0.26163 0.2677 RANDOM 27.106
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] 4.17 1.27 -2.75 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.95 r_dihedral_angle_3_deg 20.197 r_dihedral_angle_4_deg 15.429 r_dihedral_angle_1_deg 11.04 r_scangle_it 5.162 r_scbond_it 3.615 r_angle_refined_deg 2.954 r_mcangle_it 2.244 r_mcbond_it 1.336 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.95 r_dihedral_angle_3_deg 20.197 r_dihedral_angle_4_deg 15.429 r_dihedral_angle_1_deg 11.04 r_scangle_it 5.162 r_scbond_it 3.615 r_angle_refined_deg 2.954 r_mcangle_it 2.244 r_mcbond_it 1.336 r_nbtor_refined 0.33 r_symmetry_vdw_refined 0.278 r_nbd_refined 0.258 r_chiral_restr 0.253 r_xyhbond_nbd_refined 0.186 r_symmetry_hbond_refined 0.159 r_bond_refined_d 0.036 r_gen_planes_refined 0.013 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 2628 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling