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Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide bonds
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 293 35% methyl-pentanediol, 0.1M Tris pH 8.5, 0.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.85 α = 90 b = 64.788 β = 98.18 c = 74.177 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 MARMOSAIC 325 mm CCD K-B FOCUSING MIRRORS 2012-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.215 73.422 94.4 0.046 10.9 2.9 129615 2
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 1.22 1.28 83 0.568 0.568 1.2 2.6
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 3IQ6 1.22 31.94 137065 129477 9283 94.2 0.134 0.131 0.1313 0.179 0.1792 RANDOM 26.19
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.023 r_sphericity_free 40.641 r_sphericity_bonded 22.913 r_dihedral_angle_3_deg 13.899 r_rigid_bond_restr 7.363 r_dihedral_angle_1_deg 4.835 r_angle_refined_deg 3.933 r_dihedral_angle_4_deg 3.635 r_chiral_restr 0.396 r_bond_refined_d 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.023 r_sphericity_free 40.641 r_sphericity_bonded 22.913 r_dihedral_angle_3_deg 13.899 r_rigid_bond_restr 7.363 r_dihedral_angle_1_deg 4.835 r_angle_refined_deg 3.933 r_dihedral_angle_4_deg 3.635 r_chiral_restr 0.396 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3260 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 211
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing