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CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.085M AMMONIUM CITRATE, PH 5.6, 0.17M SODIUM ACETATE, 1MM MNCL2, 25% PEG 4000,15% GLYCEROL, VAPOR DIFFUSION,SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.16 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.468 α = 90 b = 85.486 β = 90 c = 141.623 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 ADSC QUANTUM 315 MIRRORS 2014-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 1.47 50 97.7 0.102 0.102 18.2 7 122409 -5
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 1.47 1.5 83.1 0.79 0.79 2.1 6.4
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 MR THROUGHOUT 4QRN 1.47 50 118586 3732 98.14 0.12151 0.12018 0.1405 0.16377 0.1732 RANDOM 21.901
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] 0.58 -0.26 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.286 r_sphericity_free 25.107 r_dihedral_angle_4_deg 17.151 r_dihedral_angle_3_deg 12.646 r_sphericity_bonded 10.268 r_dihedral_angle_1_deg 6.242 r_scbond_it 5.703 r_scbond_other 5.703 r_scangle_other 5.513 r_rigid_bond_restr 5.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.286 r_sphericity_free 25.107 r_dihedral_angle_4_deg 17.151 r_dihedral_angle_3_deg 12.646 r_sphericity_bonded 10.268 r_dihedral_angle_1_deg 6.242 r_scbond_it 5.703 r_scbond_other 5.703 r_scangle_other 5.513 r_rigid_bond_restr 5.242 r_long_range_B_refined 4.624 r_long_range_B_other 4.624 r_mcangle_other 2.752 r_mcangle_it 2.749 r_mcbond_it 2.503 r_mcbond_other 2.496 r_angle_refined_deg 1.77 r_angle_other_deg 1.009 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5559 Nucleic Acid Atoms Solvent Atoms 786 Heterogen Atoms 26
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling