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Crystal structure of the SCAN domain from human paternally expressed gene 3 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E6S PDB ENTRY 4E6S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 CRYSTALLIZATION WAS OBSERVED DURING PROTEIN CONCENTRATION USING VIVASPIN 20 CONCENTRATORS (SARTORIUS STEDIM BIOTECH) IN 50 MM TRIS-HCL PH 7.5, 150 MM NACL.
Crystal Properties Matthews coefficient Solvent content 2.44 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.615 α = 90 b = 83.615 β = 90 c = 55.233 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 287 CCD RIGAKU CCD 2013-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.95 13.8 99.7 0.07 38 28 16090 2
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 1.95 2 99.8 0.31 9.7 20.8
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 4E6S 1.95 13.82 15239 806 99.53 0.17412 0.17151 0.1802 0.22383 0.2286 RANDOM 28.167
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] 3.11 3.11 -6.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_4_deg 23.797 r_dihedral_angle_3_deg 18.328 r_dihedral_angle_1_deg 5.924 r_angle_refined_deg 2.017 r_angle_other_deg 0.961 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.025 r_dihedral_angle_4_deg 23.797 r_dihedral_angle_3_deg 18.328 r_dihedral_angle_1_deg 5.924 r_angle_refined_deg 2.017 r_angle_other_deg 0.961 r_chiral_restr 0.12 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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 1567 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing