2D3H | pdb_00002d3h

Crystal structures of collagen model peptides (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CUO	PDB 2CUO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	PEG 1000, ACETATE BUFFER, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.987	α = 90
b = 26.668	β = 90.03
c = 79.843	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	95	CCD	ADSC QUANTUM 4	1.1-M-LONG BENT-PLANE MIRROR	2004-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	0.978	Photon Factory	BL-6A

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	1.22	26.61	98.7	0.082	4.5	3.52		32577	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)
	1.22	1.26	99.8		0.287	2.2	3.79

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-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB 2CUO	1.22	8	1	32044	32044	1627		0.1964	0.1964	0.1934	0.2548	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
	823	1158

RMS Deviations
Key	Refinement Restraint Deviation
s_anti_bump_dis_restr	0.145
s_approx_iso_adps	0.076
s_zero_chiral_vol	0.059
s_non_zero_chiral_vol	0.047
s_similar_adp_cmpnt	0.046
s_from_restr_planes	0.0282
s_angle_d	0.024
s_bond_d	0.01
s_rigid_bond_adp_cmpnt	0.004
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	895
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
CrystalClear	data reduction
X-PLOR	model building
SHELXL-97	refinement
HKL-2000	data reduction
CrystalClear	data scaling
X-PLOR	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.