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Crystal Structure of the Membrane Proximal Oxidoreductase Domain of Human Steap3, the Dominant Ferric Reductase of the Erythroid Transferrin Cycle
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VNS PDB ENTRY 2VNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 0.01M FECL3, 40-100MM NA3.CITRATE, 4% V/V JEFFAMINE M600 PH5.6
Crystal Properties Matthews coefficient Solvent content 2.31 46.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.686 α = 90 b = 66.812 β = 90 c = 143.366 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 MARRESEARCH FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID FOCUSING MIRROR 2007-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.92 50 97.5 0.03 19.1 3.9 27874 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 1.92 1.99 85.1 0.27 2.8 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VNS 2 50 23736 1293 98.9 0.199 0.197 0.2327 0.236 0.2616 RANDOM 19.31
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] 0.22 1.73 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 38.944 r_dihedral_angle_2_deg 33.631 r_dihedral_angle_4_deg 20.298 r_dihedral_angle_3_deg 15.863 r_angle_other_deg 3.295 r_scangle_it 2.925 r_scbond_it 2.058 r_mcangle_it 1.673 r_mcbond_it 1.531 r_angle_refined_deg 1.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 38.944 r_dihedral_angle_2_deg 33.631 r_dihedral_angle_4_deg 20.298 r_dihedral_angle_3_deg 15.863 r_angle_other_deg 3.295 r_scangle_it 2.925 r_scbond_it 2.058 r_mcangle_it 1.673 r_mcbond_it 1.531 r_angle_refined_deg 1.498 r_symmetry_vdw_other 0.302 r_symmetry_hbond_refined 0.291 r_symmetry_vdw_refined 0.277 r_nbd_other 0.241 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.179 r_nbtor_other 0.099 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 2729 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement HKL data reduction SCALEPACK data scaling REFMAC phasing