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Rat cysteine dioxygenase with 3-mercaptopropionic acid persulfide bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ELN PDB entry 3eln
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 297 Hanging drops of 1.5 microL of approximately 8 mg/mL CDO and 1.5 microL reservoir buffer were allowed to equilibrate above the reservoir buffer (24-34% (w/v) polyethylene glycol 4000, 100-250 mM ammonium acetate, 100 mM sodium citrate, 0-4 mM dithionite, 40 mM 3-mercaptopropionic acid). Crystals grew as needles or starbursts of approximately 0.1 mm in length in one week, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.19 43.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.56 α = 90 b = 57.56 β = 90 c = 122 γ = 90
Symmetry Space Group P 43 21 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 210r Double Si with sagittaly bent second crystal 2012-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
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 1.63 52.06 100 0.025 296.1 5.4 26441 26441 1.5 18.9
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 1.63 1.72 100 0.362 27.2 7.6 3769
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3eln 1.63 30.5 26368 24606 1312 98.22 0.21095 0.20966 0.2089 0.2358 0.2344 The same R-free flags as PDB 3eln 21.299
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] -0.24 -0.24 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.929 r_dihedral_angle_4_deg 12.794 r_dihedral_angle_3_deg 12.695 r_dihedral_angle_1_deg 6.018 r_angle_refined_deg 1.262 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.929 r_dihedral_angle_4_deg 12.794 r_dihedral_angle_3_deg 12.695 r_dihedral_angle_1_deg 6.018 r_angle_refined_deg 1.262 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_scbond_it 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 1519 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 8
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling