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C-terminal domain of stomatin operon partner protein 1510-C from Pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EXD PDB ENTRY 2EXD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% Jeffamine M-600, 0.1M HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.847 α = 90 b = 75.847 β = 90 c = 43.631 γ = 120
Symmetry Space Group P 62 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r mirror 2013-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 2.4 19.57 99.7 0.077 25.9 10 3165 27.6
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 2.4 2.53 100 0.404 6.9 10.5 443
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 2EXD 2.4 18.96 2865 288 99.37 0.22464 0.22084 0.2211 0.25796 0.259 RANDOM 31.797
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] 0.05 0.03 0.05 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.748 r_dihedral_angle_4_deg 21.193 r_dihedral_angle_3_deg 15.518 r_dihedral_angle_1_deg 6.808 r_long_range_B_refined 6.385 r_mcangle_it 2.895 r_scbond_it 2.209 r_mcbond_it 1.649 r_angle_refined_deg 1.316 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.748 r_dihedral_angle_4_deg 21.193 r_dihedral_angle_3_deg 15.518 r_dihedral_angle_1_deg 6.808 r_long_range_B_refined 6.385 r_mcangle_it 2.895 r_scbond_it 2.209 r_mcbond_it 1.649 r_angle_refined_deg 1.316 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 507 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 1
Software Software Software Name Purpose XDS data scaling PHENIX model building REFMAC refinement XDS data reduction SCALA data scaling PHENIX phasing