9J1R

Structure of a triple-helix region of human Collagen type II from Trautec

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K6F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Crystal-C7:0.2M (NH4)2SO4, 30% PEG4,000

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.777	α = 90
b = 14.204	β = 105.826
c = 48.46	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	PIXEL	DECTRIS PILATUS3 6M		2024-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	0.99999	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.45	46.62	97.8	0.999	16.7	6.6		11458

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47			0.826

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1K6F	1.45	46.62	11457	578	97.957	0.185	0.1831	0.2235	24.276

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]
-1.422		0.234	-1.549		2.446

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	17.73
r_dihedral_angle_6_deg	17.482
r_lrange_other	15.913
r_scangle_it	12.153
r_scangle_other	11.871
r_dihedral_angle_3_deg	11.766
r_mcangle_other	10.293
r_mcangle_it	10.283
r_scbond_it	8.533
r_scbond_other	8.192
r_dihedral_angle_2_deg	8.089
r_mcbond_it	7.173
r_mcbond_other	7.129
r_dihedral_angle_1_deg	5.837
r_rigid_bond_restr	4.489
r_angle_refined_deg	1.951
r_angle_other_deg	0.678
r_symmetry_xyhbond_nbd_other	0.428
r_symmetry_xyhbond_nbd_refined	0.301
r_xyhbond_nbd_refined	0.291
r_nbd_refined	0.218
r_nbd_other	0.206
r_symmetry_nbd_refined	0.201
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.182
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	575
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing