9P17 | pdb_00009p17

Thermolysin Room-Temperature In-Situ, Shipped

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DLH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.20 M sodium di-hydrogen phosphate, 16.7% polyethylene glycol (PEG) 3350

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.032	α = 90
b = 93.032	β = 90
c = 130.452	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER2 X 4M		2024-09-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE VMXi	0.7749	Diamond	VMXi

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.66	80.57	98.8	0.132	0.143	0.054	0.998	11.2	10.9		39612

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.66	1.69	91		1.611	1.934	1.024	0.368	0.5	4.6

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	1.66	80.568	39545	1991	98.865	0.162	0.1605	0.1604	0.1831	0.1831	21.317

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]
-0.164	-0.082		-0.164		0.534

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.05
r_dihedral_angle_3_deg	13.061
r_lrange_it	10.977
r_dihedral_angle_2_deg	6.508
r_dihedral_angle_1_deg	6.171
r_scangle_it	5.03
r_scbond_it	3.218
r_mcangle_it	2.324
r_angle_refined_deg	1.78
r_mcbond_it	1.71
r_symmetry_nbd_refined	0.331
r_nbtor_refined	0.323
r_symmetry_xyhbond_nbd_refined	0.272
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.095
r_metal_ion_refined	0.089
r_gen_planes_refined	0.012
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2420
Nucleic Acid Atoms
Solvent Atoms	228
Heterogen Atoms	11

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
Coot	model building
xia2.multiplex	data reduction
MOLREP	phasing