5XH2 | pdb_00005xh2

Crystal structure of a novel PET hydrolase R103G/S131A mutant in complex with pNP from Ideonella sakaiensis 201-F6

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	Ammonium Sulfate, NaCl, HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.784	α = 90
b = 51.532	β = 90
c = 84.373	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300-HS		2017-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.9998	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.2	25	99.8	0.05	0.053	0.019	10	8		69716

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	1.2	1.24	98.9		0.212	0.228	0.081	0.982		7.6

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 (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	4WFI	1.2	25	66256	3391	99.59	0.0997	0.0984	0.11	0.1246	0.13	RANDOM	10.757

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]
-0.3			0.29		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.729
r_sphericity_free	26.525
r_dihedral_angle_4_deg	17.151
r_dihedral_angle_3_deg	10.441
r_sphericity_bonded	9.793
r_rigid_bond_restr	7.103
r_dihedral_angle_1_deg	6.596
r_angle_refined_deg	1.489
r_angle_other_deg	0.821
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.729
r_sphericity_free	26.525
r_dihedral_angle_4_deg	17.151
r_dihedral_angle_3_deg	10.441
r_sphericity_bonded	9.793
r_rigid_bond_restr	7.103
r_dihedral_angle_1_deg	6.596
r_angle_refined_deg	1.489
r_angle_other_deg	0.821
r_chiral_restr	0.106
r_gen_planes_refined	0.014
r_bond_refined_d	0.011
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1912
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	30

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing
HKL	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.