9I5B | pdb_00009i5b

Crystal structure of perlecan region 3 mutant (P1019L) construct I876-V1272 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
3.79	67.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.65	α = 75.235
b = 74.968	β = 73.124
c = 81.368	γ = 80.112

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	2.52	47.67	98.5	0.994	9.9	3.6		41874

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	2.52	2.58			0.645

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	2.52	47.67	41722	1993	98.545	0.19	0.1883	0.1883	0.2202	0.2203	58.623

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]
-3.371	1.5	0.306	-1.314	-2.903	3.458

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.386
r_dihedral_angle_6_deg	14.258
r_lrange_it	10.07
r_dihedral_angle_1_deg	7.82
r_scangle_it	7.035
r_dihedral_angle_2_deg	6.725
r_mcangle_it	4.888
r_scbond_it	4.578
r_mcbond_it	3.073
r_angle_refined_deg	1.87
r_nbtor_refined	0.31
r_symmetry_nbd_refined	0.251
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.163
r_chiral_restr	0.127
r_ncsr_local_group_1	0.089
r_bond_refined_d	0.008
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5063
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	16

Software

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