☰ Navigation Tabs
Crystal structure of a 40 kDa signalling protein from Porcine (SPP-40) at 2.89A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OWQ PDB entry 1OWQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 25mM tris-HCl, 50mM NaCl, 20% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.75 α = 90 b = 66.454 β = 90 c = 107.652 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 293 IMAGE PLATE MARRESEARCH MIRROR 2004-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5412
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 2.89 56 90.7 0.13 3.3 7.3 10510 9476 36.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.89 3 87.1 0.542 1.3
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1OWQ 2.9 56 9476 9026 450 90.22 0.18 0.17911 0.17723 0.21765 RANDOM 28.47
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] -0.91 -0.97 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.681 r_scangle_it 5.032 r_dihedral_angle_1_deg 3.142 r_scbond_it 3.058 r_mcangle_it 2.528 r_angle_refined_deg 2.015 r_angle_other_deg 1.486 r_mcbond_it 1.355 r_symmetry_vdw_other 0.461 r_nbtor_other 0.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.681 r_scangle_it 5.032 r_dihedral_angle_1_deg 3.142 r_scbond_it 3.058 r_mcangle_it 2.528 r_angle_refined_deg 2.015 r_angle_other_deg 1.486 r_mcbond_it 1.355 r_symmetry_vdw_other 0.461 r_nbtor_other 0.393 r_symmetry_vdw_refined 0.356 r_nbd_refined 0.281 r_nbd_other 0.259 r_symmetry_hbond_refined 0.228 r_xyhbond_nbd_refined 0.164 r_chiral_restr 0.117 r_xyhbond_nbd_other 0.086 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 2875 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing