☰ Navigation Tabs
Crystal Structure of N-Phenylalanine Peptoid-modified Collagen Triple Helix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JX4 7jx4.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 0.3 micro-l protein (NlysX-CMP7 [Ac-(GlyProHyp)3-GlyNpheHyp-(GlyProHyp)3]) in water at 10 mg/ml, mixed with 0.3 micro-l crystallization buffer containing 2.4 M sodium malonate dibasic monohydrate.
Crystal Properties Matthews coefficient Solvent content 1.86 33.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.442 α = 88.72 b = 31.332 β = 74.96 c = 35.408 γ = 89.79
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2018-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.1 34.19 90.6 0.107 0.111 0.029 0.999 17.8 14.1 31530
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.12 66.3 4.146 4.334 1.237 0.459 11.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7jx4.pdb 1.1 34.19 29490 2021 90.52 0.1544 0.1513 0.1981 0.1923 RANDOM 14.639
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] 0.25 -0.67 -0.64 1 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 11.941 r_dihedral_angle_1_deg 6.799 r_rigid_bond_restr 5.062 r_angle_refined_deg 2.01 r_angle_other_deg 0.751 r_chiral_restr 0.073 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 384 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 744
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing