9J23

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	Index-G12:0.2M MgCl2, 0.1M HEPES pH7.5, 25% PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
1.98	33.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.987	α = 90
b = 20.042	β = 99.984
c = 44.985	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		2024-07-15	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	1.75	44.3	99.7	0.908	3.5	5.6		6457

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	1.75	1.78			0.812

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	1.75	44.3	6450	299	99.737	0.243	0.2407	0.2879	15.135

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]
0.743		0.446	1.249		-2.023

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.645
r_dihedral_angle_3_deg	9.992
r_dihedral_angle_2_deg	6.887
r_dihedral_angle_1_deg	5.711
r_lrange_it	4.287
r_lrange_other	4.133
r_scangle_it	2.615
r_scangle_other	2.612
r_mcangle_it	2.172
r_mcangle_other	2.169
r_scbond_it	1.646
r_scbond_other	1.643
r_angle_refined_deg	1.489
r_mcbond_it	1.314
r_mcbond_other	1.312
r_angle_other_deg	0.432
r_xyhbond_nbd_refined	0.195
r_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.181
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.164
r_nbd_other	0.149
r_symmetry_nbd_refined	0.114
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.061
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	554
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms

Software

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