9J1T

Structure of a triple-helix region of human Collagen type IV 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-C4:0.2M NaAc, 0.1M Sodium cacodylate pH6.5, 30% PEG8,000

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.316	α = 90
b = 17.717	β = 101.194
c = 65.821	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	32.28	96.4	0.998	17.9	6.7		11714

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			0.989

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	32.28	11707	531	95.661	0.192	0.1902	0.2204	16.157

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]
-0.612		-0.395	-0.802		1.456

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.118
r_dihedral_angle_3_deg	10.646
r_dihedral_angle_1_deg	5.916
r_lrange_it	5.288
r_lrange_other	4.883
r_dihedral_angle_2_deg	4.277
r_mcangle_it	3.236
r_mcangle_other	3.233
r_scangle_it	3.102
r_scangle_other	3.098
r_scbond_it	2.124
r_scbond_other	2.12
r_mcbond_it	2.037
r_mcbond_other	2.037
r_angle_refined_deg	1.849
r_angle_other_deg	0.569
r_nbd_refined	0.207
r_symmetry_xyhbond_nbd_refined	0.204
r_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.179
r_nbd_other	0.139
r_ncsr_local_group_1	0.129
r_ncsr_local_group_3	0.1
r_symmetry_nbtor_other	0.094
r_ncsr_local_group_2	0.084
r_chiral_restr	0.069
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_chiral_restr_other	0.009
r_symmetry_nbd_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	481
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	6

Software

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