9J26 | pdb_00009j26

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	Index-D5:0.1M NaAc pH4.5, 25% PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
1.76	30.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 13.982	α = 86.62
b = 30.428	β = 86.473
c = 68.051	γ = 89.284

Symmetry
Space Group	P 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	33.9	95.6	0.992	11.1	3.4		18950

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	1.48			0.98

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1K6F	1.45	33.9	18949	801	95.591	0.164	0.1615	0.17	0.2106	0.21	15.735

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]
0.089	0.409	-0.543	-1.283	0.194	1.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.34
r_dihedral_angle_3_deg	10.527
r_dihedral_angle_1_deg	5.861
r_dihedral_angle_2_deg	5.522
r_lrange_it	4.827
r_lrange_other	4.56
r_scangle_it	3.201
r_scangle_other	3.199
r_mcangle_it	2.703
r_mcangle_other	2.702
r_scbond_it	2.155
r_scbond_other	2.153
r_mcbond_it	1.821
r_mcbond_other	1.817
r_angle_refined_deg	1.645
r_angle_other_deg	0.55
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_refined	0.194
r_symmetry_nbd_refined	0.194
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.167
r_nbd_other	0.152
r_ncsr_local_group_4	0.144
r_ncsr_local_group_1	0.141
r_ncsr_local_group_10	0.138
r_ncsr_local_group_2	0.131
r_ncsr_local_group_15	0.129
r_ncsr_local_group_13	0.122
r_ncsr_local_group_11	0.121
r_ncsr_local_group_5	0.12
r_ncsr_local_group_14	0.12
r_ncsr_local_group_6	0.118
r_ncsr_local_group_9	0.108
r_ncsr_local_group_8	0.104
r_ncsr_local_group_7	0.1
r_ncsr_local_group_12	0.095
r_ncsr_local_group_3	0.093
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.071
r_chiral_restr_other	0.06
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1117
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms

Software

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