☰ Navigation Tabs
Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Sequence at 1.3 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other (Pro-Hyp-Gly)10 structure reported in V.Nagarajan, S.Kamitori and K.Okuyama, J.Biochem., 125, 310 (1999).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 PEG 200, Acetic acid, Sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.87 34.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 14.051 α = 90 b = 26.775 β = 106.76 c = 20.004 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC QUANTUM 4 1-M-LONG BENT-CYLINDER MIRROR 2002-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL40B2 1.00 SPring-8 BL40B2
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 1.25 19.15 94.5 0.057 7.6 3.4 3768 1 1
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 1.25 1.3 67.7 0.235 2.4 268
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT (Pro-Hyp-Gly)10 structure reported in V.Nagarajan, S.Kamitori and K.Okuyama, J.Biochem., 125, 310 (1999). 1.25 10 4 3733 3547 186 89.1 0.1346 0.1886 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 112 175
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.093 s_similar_adp_cmpnt 0.037 s_non_zero_chiral_vol 0.033 s_from_restr_planes 0.0314 s_angle_d 0.023 s_bond_d 0.018 s_anti_bump_dis_restr 0.014 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 133 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection CrystalClear data reduction SHELX model building SHELXL-97 refinement CrystalClear data scaling SHELX phasing