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Crystal structure of the siroheme decarboxylase NirDL in co-complex with iron-uroporphyrin III analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CH7 PDB ENTRY 4CH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 FOR THE CRYSTALLIZATION OF THE NIRDL-FE-URO III CO-COMPLEX, NIRDL (7 MG/ML) WAS INCUBATED 30 MIN ON ICE WITH 0.5 MM FE-URO III (DISSOLVED IN 50 % DMSO) PRIOR TO CRYSTAL SETUP. PROTEIN-FE-URO III WAS MIXED WITH EQUAL AMOUNTS OF PRECIPITANT SOLUTION (27 % (V/V) MPD, 0.1 M MES, PH 5.5, AND 9.95 MM SPERMIDINE). CRYSTALS WERE CRYO-PROTECTED WITH 25-33 % (V/V) GLYCEROL OR ADDITIONAL 33 % (V/V) MPD PRIOR TO FLASH FREEZING IN LIQUID NITROGEN.
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.75 α = 90 b = 72.6 β = 102.06 c = 51.11 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU SATURN 944PLUS 2012-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.9 28.7 97.8 0.04 22.7 3.1 8137 2.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 92.6 0.44 2.57 2.8
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 4CH7 2.9 28.68 7730 407 97.78 0.23215 0.22939 0.2307 0.28432 0.2789 RANDOM 51.182
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] 0.25 -4.75 2.43 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.713 r_dihedral_angle_3_deg 15.678 r_dihedral_angle_4_deg 13.711 r_dihedral_angle_1_deg 6.338 r_mcangle_it 6.167 r_scbond_it 4.368 r_mcbond_it 3.693 r_mcbond_other 3.685 r_angle_refined_deg 1.657 r_angle_other_deg 0.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.713 r_dihedral_angle_3_deg 15.678 r_dihedral_angle_4_deg 13.711 r_dihedral_angle_1_deg 6.338 r_mcangle_it 6.167 r_scbond_it 4.368 r_mcbond_it 3.693 r_mcbond_other 3.685 r_angle_refined_deg 1.657 r_angle_other_deg 0.769 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 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_mcangle_other 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 2507 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing