8ZMV

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Index-H6 (0.2M Sodium formate, 20% PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.96	α = 90
b = 13.757	β = 100.116
c = 66.084	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 EIGER X 9M		2024-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95300	CLSI	08ID-1

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	32.53	98.7	0.998	15.2	6.5		11135

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			0.634

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.45	32.53	11131	1134	98.644	0.237	0.2303	0.2984	25.61

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]
-0.592		-4.467	-0.022		2.075

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	20.893
r_lrange_it	15.026
r_lrange_other	14.309
r_dihedral_angle_3_deg	9.134
r_scangle_it	9.112
r_scangle_other	9.101
r_mcangle_it	9.021
r_mcangle_other	9.021
r_mcbond_it	6.331
r_scbond_it	6.312
r_scbond_other	6.299
r_mcbond_other	6.289
r_dihedral_angle_1_deg	5.503
r_rigid_bond_restr	4.682
r_angle_refined_deg	1.573
r_angle_other_deg	0.527
r_symmetry_nbd_refined	0.256
r_nbd_other	0.206
r_nbd_refined	0.205
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.158
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.07
r_chiral_restr_other	0.017
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	548
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms

Software

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