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Crystal structure of phenolic acid decarboxylase (2635953) from Bacillus subtilis at 1.36 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CG9 PDB entry 2CG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 277 NANODROP, 0.2M NaCl, 10.0% PEG 8000, 1.0M LiCl, 20.0% PEG 6000, 0.1M Na,K Phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.46 64.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.475 α = 90 b = 117.475 β = 90 c = 117.475 γ = 90
Symmetry Space Group P 41 3 2
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 ADSC QUANTUM 315 2006-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.00000 ALS 5.0.3
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 1.36 58.722 99.6 0.107 0.107 5.6 18.2 59580
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 1.36 1.43 97.4 0.01 1.036 0.7 8.1 8323
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2CG9 1.36 58.722 59375 2999 99.35 0.134 0.134 0.133 0.146 0.1628 RANDOM 14.486
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 34.902 r_dihedral_angle_4_deg 14.996 r_dihedral_angle_3_deg 10.437 r_dihedral_angle_1_deg 6.828 r_scangle_it 5.662 r_scbond_it 3.713 r_mcangle_it 2.135 r_mcbond_it 1.666 r_angle_refined_deg 1.489 r_angle_other_deg 0.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.902 r_dihedral_angle_4_deg 14.996 r_dihedral_angle_3_deg 10.437 r_dihedral_angle_1_deg 6.828 r_scangle_it 5.662 r_scbond_it 3.713 r_mcangle_it 2.135 r_mcbond_it 1.666 r_angle_refined_deg 1.489 r_angle_other_deg 0.847 r_mcbond_other 0.353 r_symmetry_vdw_other 0.278 r_symmetry_vdw_refined 0.23 r_nbd_other 0.21 r_nbd_refined 0.203 r_nbtor_refined 0.197 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.093 r_nbtor_other 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1348 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 32
Software Software Software Name Purpose MolProbity model building REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction ADSC data collection MOSFLM data reduction CCP4 data scaling PHASER phasing