9I5A | pdb_00009i5a

Crystal structure of wild type perlecan region 3 construct I876-V1272 construct including one laminin IV-like and four laminin EGF-like domains.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	RoseTTAFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295.15	0.85M succinic acid, pH 7

Crystal Properties
Matthews coefficient	Solvent content
3.65	66.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.637	α = 74.384
b = 74.612	β = 74.084
c = 78.769	γ = 79.729

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 EIGER X 16M		2024-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.7293	MAX IV	BioMAX

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	2.04	47.32	98.3	0.997	9.7	3.6		75120

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	2.04	2.1			0.669

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.045	46.244	75118	2000	98.343	0.178	0.1777	0.1778	0.2086	0.2086	61.621

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]
-2.89	0.819	1.058	-1	-2.239	3.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.807
r_dihedral_angle_6_deg	13.751
r_dihedral_angle_2_deg	9.555
r_lrange_it	9.337
r_lrange_other	9.313
r_dihedral_angle_1_deg	7.349
r_scangle_it	6.317
r_scangle_other	6.316
r_mcangle_it	4.62
r_mcangle_other	4.619
r_scbond_it	4.092
r_scbond_other	4.091
r_mcbond_it	3.009
r_mcbond_other	3.008
r_angle_refined_deg	1.583
r_angle_other_deg	0.568
r_nbd_other	0.222
r_symmetry_nbd_other	0.207
r_xyhbond_nbd_refined	0.204
r_nbd_refined	0.201
r_symmetry_xyhbond_nbd_refined	0.201
r_symmetry_nbd_refined	0.199
r_nbtor_refined	0.172
r_ncsr_local_group_1	0.105
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5635
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing