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Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 293 PEG 400, TRIS, OCTYL-BETA-D-GLUCOPYRANOSIDE, SODIUM AZIDE, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.31 62.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.78 α = 90 b = 124.145 β = 90 c = 129.609 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2002-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 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 2.15 33.2 98.7 0.048 8.7 10.7 24593 24593 32.2
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 2.15 2.28 93.7 0.367 2.1 8.2 3266
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SIRAS THROUGHOUT 2.15 33 24591 24591 1253 98.69 0.19093 0.19093 0.18951 0.1856 0.21747 0.2112 RANDOM 39.491
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] 1.92 0.19 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.917 r_dihedral_angle_3_deg 15.199 r_dihedral_angle_4_deg 14.684 r_dihedral_angle_1_deg 5.519 r_scangle_it 4.702 r_scbond_it 2.973 r_angle_refined_deg 1.719 r_mcangle_it 1.632 r_mcbond_it 1.049 r_angle_other_deg 0.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.917 r_dihedral_angle_3_deg 15.199 r_dihedral_angle_4_deg 14.684 r_dihedral_angle_1_deg 5.519 r_scangle_it 4.702 r_scbond_it 2.973 r_angle_refined_deg 1.719 r_mcangle_it 1.632 r_mcbond_it 1.049 r_angle_other_deg 0.539 r_nbtor_refined 0.308 r_nbd_other 0.287 r_symmetry_vdw_refined 0.25 r_nbtor_other 0.239 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.117 r_mcbond_other 0.032 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SHARP phasing