9J8I | pdb_00009j8i

Mutant of a deep sea bacterial PET hydrolase MtCut

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	800 mM (NH4)2SO4, 100 mM Sodium citrate/Citric acid pH4.0

Crystal Properties
Matthews coefficient	Solvent content
4.89	74.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.94	α = 90
b = 187.94	β = 90
c = 132.02	γ = 90

Symmetry
Space Group	P 42 21 2

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	STFC Large Pixel Detector		2024-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

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	2.72	32.53	99.9	0.328	0.332	0.051	0.996	14.6	42.4		63825

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	2.72	2.79		100	3.448	3.486	0.517	0.75		45.2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.72	32.53	60541	3229	99.88	0.1908	0.18856	0.1965	0.23238	0.2383	RANDOM	60.698

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]
-2.76			-2.76		5.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.217
r_dihedral_angle_2_deg	9.127
r_long_range_B_other	8.397
r_long_range_B_refined	8.396
r_dihedral_angle_1_deg	7.217
r_scangle_other	7.106
r_mcangle_other	6.478
r_mcangle_it	6.477
r_scbond_it	5.148
r_scbond_other	5.148
r_mcbond_it	4.697
r_mcbond_other	4.696
r_angle_refined_deg	1.805
r_angle_other_deg	0.618
r_chiral_restr	0.08
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7992
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
xia2	data reduction