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CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE LIGW2 FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 (TARGET EFI-505250) WITH BOUND MANGANESE AND 3-methoxy-4-hydroxy-5-nitrobenzoic acid, THE D314N MUTANT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4INF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.085M SODIUM CITRATE, PH 5.6, 0.17M SODIUM ACETATE, 25% PEG 4000,15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 1.97 37.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.159 α = 90 b = 60.59 β = 112.84 c = 123.473 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 CCD ADSC QUANTUM 315 MIRRORS 2014-04-04 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 1.8 50 99.9 0.141 0.141 8.9 3.7 123052 -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 1.8 1.83 99.7 0.85 0.85 1.8 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4INF 1.8 50 119106 3711 99.83 0.15742 0.15577 0.20999 0.2176 RANDOM 23.92
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] -0.42 0.86 -0.36 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.794 r_dihedral_angle_4_deg 17.236 r_dihedral_angle_3_deg 13.727 r_scbond_it 13.657 r_scbond_other 13.656 r_scangle_other 12.968 r_long_range_B_refined 12.135 r_long_range_B_other 12.134 r_dihedral_angle_1_deg 5.875 r_mcangle_other 4.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.794 r_dihedral_angle_4_deg 17.236 r_dihedral_angle_3_deg 13.727 r_scbond_it 13.657 r_scbond_other 13.656 r_scangle_other 12.968 r_long_range_B_refined 12.135 r_long_range_B_other 12.134 r_dihedral_angle_1_deg 5.875 r_mcangle_other 4.993 r_mcangle_it 4.989 r_mcbond_it 4.807 r_mcbond_other 4.763 r_angle_refined_deg 1.431 r_angle_other_deg 0.813 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11114 Nucleic Acid Atoms Solvent Atoms 1155 Heterogen Atoms 122
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling