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Cartilage homing cysteine-dense-peptides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ATM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2M Ammonium sulfate, 20% PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.24 α = 90 b = 34.927 β = 90 c = 36.977 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 100 CCD RIGAKU SATURN 944 2017-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.76 50 78.3 0.078 0.023 35.4 10.7 2368
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79 8.1 0.145 0.094 0.991 8.5 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 6ATM 1.78 25.39 2207 139 84.72 0.11289 0.10984 0.1226 0.16451 0.1618 RANDOM 10.753
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] 0.2 -0.09 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 24.703 r_dihedral_angle_2_deg 21.848 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_1_deg 6.968 r_long_range_B_other 3.589 r_long_range_B_refined 3.585 r_angle_refined_deg 1.874 r_scangle_other 1.666 r_scbond_it 1.598 r_scbond_other 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 24.703 r_dihedral_angle_2_deg 21.848 r_dihedral_angle_3_deg 12.572 r_dihedral_angle_1_deg 6.968 r_long_range_B_other 3.589 r_long_range_B_refined 3.585 r_angle_refined_deg 1.874 r_scangle_other 1.666 r_scbond_it 1.598 r_scbond_other 1.12 r_angle_other_deg 1.08 r_mcangle_other 0.932 r_mcangle_it 0.931 r_mcbond_it 0.673 r_mcbond_other 0.667 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_bond_other_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 290 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing