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Structure of the reversible pyrrole-2-carboxylic acid decarboxylase PA0254/HudA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IWS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.12 M alcohols, 0.1 M imidazole/MES pH 6.5, 20% v/v glycerol and 10% w/v PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.7 54.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.81 α = 90 b = 55.48 β = 99.92 c = 199.53 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 PIXEL DECTRIS PILATUS3 R CdTe 300K 2017-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.63 54 96.4 0.093 1 8.6 3.1 279939
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.67 86 0.812 0.7 1.5
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 4IWS 1.65 53.64 265205 14039 99.61 0.20311 0.20145 0.2124 0.23475 0.241 RANDOM 19.082
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] 1.06 0.4 -1.1 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.867 r_dihedral_angle_4_deg 18.993 r_dihedral_angle_3_deg 14.19 r_dihedral_angle_1_deg 6.77 r_angle_refined_deg 2.124 r_angle_other_deg 1.012 r_chiral_restr 0.164 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.867 r_dihedral_angle_4_deg 18.993 r_dihedral_angle_3_deg 14.19 r_dihedral_angle_1_deg 6.77 r_angle_refined_deg 2.124 r_angle_other_deg 1.012 r_chiral_restr 0.164 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15347 Nucleic Acid Atoms Solvent Atoms 1424 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing