1V6Q

Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Sequence at 1.3 A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOther(Pro-Hyp-Gly)10 structure reported in V.Nagarajan, S.Kamitori and K.Okuyama, J.Biochem., 125, 310 (1999).

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277PEG 200, Acetic acid, Sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.8734.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 14.051α = 90
b = 26.775β = 106.76
c = 20.004γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDADSC QUANTUM 41-M-LONG BENT-CYLINDER MIRROR2002-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL40B21.00SPring-8BL40B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2519.1594.50.0577.63.4376811
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.367.70.2352.4268

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT(Pro-Hyp-Gly)10 structure reported in V.Nagarajan, S.Kamitori and K.Okuyama, J.Biochem., 125, 310 (1999).1.251043733354718689.10.13460.1886RANDOM
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 MethodRefinement High ResolutionRefinement Low Resolution
112175
RMS Deviations
KeyRefinement Restraint Deviation
s_zero_chiral_vol0.093
s_similar_adp_cmpnt0.037
s_non_zero_chiral_vol0.033
s_from_restr_planes0.0314
s_angle_d0.023
s_bond_d0.018
s_anti_bump_dis_restr0.014
s_rigid_bond_adp_cmpnt0.005
s_similar_dist
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms133
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
CrystalCleardata reduction
SHELXmodel building
SHELXL-97refinement
CrystalCleardata scaling
SHELXphasing