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Crystal structures of collagen model peptides with pro-hyp-gly sequence at 1.3A
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, 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 1.8 31.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 13.864 α = 90 b = 26.181 β = 105.75 c = 19.877 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 100 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 1.0 SPring-8 BL40B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.26 20 98 0.06 0.035 3.3 6.67 3592 3520 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 1.26 1.32 79 0.19 3.3 4.66 419
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, K.Okuyama, J.Biochem. 125, 310 (1999) 1.26 10 4 3520 3344 176 95 0.1332 0.159 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 112 182
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.08 s_non_zero_chiral_vol 0.059 s_bond_d 0.055 s_similar_adp_cmpnt 0.035 s_from_restr_planes 0.0336 s_angle_d 0.024 s_anti_bump_dis_restr 0.011 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 49 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection CrystalClear data reduction SHELX model building SHELXL-97 refinement CrystalClear data scaling X-PLOR phasing