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SPFH domain of mouse stomatin (Crystal form 3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 5% ethanol, 0.02 cadmium sulfate, 0.1 HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.489 α = 90 b = 84.489 β = 90 c = 68.937 γ = 120
Symmetry Space Group P 64 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 100 CCD RAYONIX MX-225 mirrors 2009-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918410 BESSY 14.1
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 1.7 73.17 99.7 0.041 33.25 11.6 16540 16492 -3 -3 37.736
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 1.7 1.8 98.7 0.871 2.97 11.5 2576
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 (All) 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 4FVF 1.8 73.17 13291 13259 704 99.76 0.19592 0.19592 0.19356 0.268 0.24512 0.3111 RANDOM 35.724
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 0.12 0.24 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.951 r_dihedral_angle_4_deg 14.344 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 5.83 r_scangle_it 4.727 r_scbond_it 3.12 r_angle_refined_deg 1.986 r_mcangle_it 1.967 r_mcbond_it 1.319 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.951 r_dihedral_angle_4_deg 14.344 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 5.83 r_scangle_it 4.727 r_scbond_it 3.12 r_angle_refined_deg 1.986 r_mcangle_it 1.967 r_mcbond_it 1.319 r_chiral_restr 0.15 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 834 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 2
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction