7Z6T | pdb_00007z6t

Aspergillus clavatus M36 protease without the propeptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4K90

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M HEPES pH 7.5, 0.2 M lithium sulfate, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.826	α = 90
b = 85.037	β = 111.303
c = 55.319	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 16M		2021-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9762	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	1.51	45.04	98.72	0.8	12.25	6.3		71273

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	1.51	1.564			0.2

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	4k90	1.51	45.04	71273	3523	97.131	0.178	0.1775	0.1622	0.196	0.1708	22.884

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]
1.64		0.747	-1.571		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.608
r_dihedral_angle_4_deg	19.682
r_dihedral_angle_3_deg	13.669
r_lrange_it	7.393
r_dihedral_angle_1_deg	6.19
r_scangle_it	4.143
r_scbond_it	3.033
r_mcangle_it	2.359
r_angle_refined_deg	1.701
r_mcbond_it	1.577
r_nbtor_refined	0.321
r_symmetry_nbd_refined	0.236
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.207
r_chiral_restr	0.109
r_symmetry_metal_ion_refined	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2994
Nucleic Acid Atoms
Solvent Atoms	449
Heterogen Atoms	186

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
Coot	model building
PHASER	phasing