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The crystal structure of the signature domain of cartilage oligomeric matrix protein.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UX6 PDB ENTRY 1UX6 AND 1YO8 experimental model PDB 1YO8 PDB ENTRY 1UX6 AND 1YO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 50mM Ammonium Sulfate,
0.05M Bis-Tris,
30% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH), pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 4.23 70.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.242 α = 90 b = 192.242 β = 90 c = 145.681 γ = 120
Symmetry Space Group P 32 2 1
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 ADSC QUANTUM 315 mirror 2008-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97945 APS 19-ID
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 3.15 39 99.9 0.133 15.4 6 53862 53862
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 3.15 3.26 100 0.88 2.3 6 5338
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 PDB ENTRY 1UX6 AND 1YO8 3.15 39 51068 51068 2735 99.73 0.2054 0.2054 0.2023 0.2038 0.2663 0.2672 RANDOM 55.482
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] 0.16 0.08 0.16 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.991 r_dihedral_angle_3_deg 20.007 r_dihedral_angle_4_deg 19.045 r_dihedral_angle_1_deg 7.246 r_scangle_it 2.949 r_scbond_it 1.709 r_angle_refined_deg 1.632 r_mcangle_it 1.047 r_mcbond_it 0.493 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.991 r_dihedral_angle_3_deg 20.007 r_dihedral_angle_4_deg 19.045 r_dihedral_angle_1_deg 7.246 r_scangle_it 2.949 r_scbond_it 1.709 r_angle_refined_deg 1.632 r_mcangle_it 1.047 r_mcbond_it 0.493 r_chiral_restr 0.119 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 12483 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 288
Software Software Software Name Purpose SBC-Collect data collection MOLREP phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling