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Crystal Structure of the buffalo Secretory Signalling Glycoprotein at 2.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ESC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 TRIS-HCL, NACL, 19% ETHANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.1 α = 90 b = 66.859 β = 90 c = 108.543 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 278 IMAGE PLATE MARRESEARCH MIRROR 2003-12-10 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 2.8 20 97.1 0.12 11 11349 43
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 2.8 2.85 95.5 0.43 2.7
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ESC 2.8 20 11349 10804 545 100 0.18852 0.18843 0.18572 0.23619 0.1793 RANDOM 34.29
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] -2.43 -0.05 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.026 r_scangle_it 4.874 r_scbond_it 2.961 r_mcangle_it 2.662 r_dihedral_angle_1_deg 2.003 r_angle_refined_deg 1.865 r_angle_other_deg 1.594 r_mcbond_it 1.441 r_nbtor_other 0.778 r_symmetry_vdw_refined 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.026 r_scangle_it 4.874 r_scbond_it 2.961 r_mcangle_it 2.662 r_dihedral_angle_1_deg 2.003 r_angle_refined_deg 1.865 r_angle_other_deg 1.594 r_mcbond_it 1.441 r_nbtor_other 0.778 r_symmetry_vdw_refined 0.59 r_symmetry_hbond_refined 0.35 r_symmetry_vdw_other 0.31 r_nbd_refined 0.268 r_nbd_other 0.252 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.119 r_xyhbond_nbd_other 0.052 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 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 2894 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing