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Crystal structure of a 40 KDa protective signalling protein from Bovine (SPC-40) at 2.1 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 25mM TRIS-HCL, 50mM NACL, 19% ETHANOL , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.78 55.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.683 α = 90 b = 67.417 β = 90 c = 106.9 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 298 IMAGE PLATE MARRESEARCH MIRROR 2003-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.1 20 97.8 0.077 8.8 27796 27796
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 2.1 2.18 97.8 0.447 2
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 1LJY 2.1 20 27796 25190 1324 97.78 0.17573 0.17342 0.1801 0.22021 0.1877 RANDOM 36.152
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] -0.22 -0.12 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.373 r_dihedral_angle_1_deg 4.874 r_scangle_it 4.25 r_scbond_it 2.58 r_angle_refined_deg 2.042 r_mcangle_it 1.982 r_angle_other_deg 1.494 r_mcbond_it 1.034 r_nbtor_other 0.561 r_nbd_refined 0.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.373 r_dihedral_angle_1_deg 4.874 r_scangle_it 4.25 r_scbond_it 2.58 r_angle_refined_deg 2.042 r_mcangle_it 1.982 r_angle_other_deg 1.494 r_mcbond_it 1.034 r_nbtor_other 0.561 r_nbd_refined 0.238 r_nbd_other 0.226 r_symmetry_vdw_refined 0.21 r_symmetry_vdw_other 0.209 r_chiral_restr 0.176 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.145 r_xyhbond_nbd_other 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002 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_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 2874 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS refinement