8ZMM

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	1K6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Index-E7 (0.05M MgCl2, 0.1M HEPES pH7.5, 30% PEG 550 MME)

Crystal Properties
Matthews coefficient	Solvent content
1.75	29.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.479	α = 90
b = 26.425	β = 99.088
c = 67.617	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	1.3	33.38	98.8	0.993	9.7	6.4		26186

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	1.3	1.32			0.609

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	1.3	33.38	26160	1294	98.472	0.146	0.1437	0.1971	15.177

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]
0.373		-0.281	0.145		-0.408

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	19.399
r_lrange_it	15.081
r_lrange_other	13.375
r_scangle_it	9.687
r_scangle_other	9.681
r_dihedral_angle_3_deg	9.633
r_mcangle_other	7.985
r_mcangle_it	7.98
r_scbond_it	6.647
r_scbond_other	6.642
r_dihedral_angle_2_deg	6.248
r_mcbond_it	5.538
r_mcbond_other	5.451
r_dihedral_angle_1_deg	5.374
r_rigid_bond_restr	4.135
r_angle_refined_deg	1.69
r_angle_other_deg	0.628
r_symmetry_xyhbond_nbd_refined	0.225
r_xyhbond_nbd_refined	0.219
r_chiral_restr_other	0.218
r_nbd_other	0.218
r_nbd_refined	0.206
r_nbtor_refined	0.184
r_symmetry_nbd_other	0.179
r_symmetry_nbd_refined	0.157
r_symmetry_nbtor_other	0.09
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr	0.067
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1064
Nucleic Acid Atoms
Solvent Atoms	235
Heterogen Atoms

Software

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