9EWR | pdb_00009ewr

Crystal structure of an inverse charged cutinase mutant from Saccharopolyspora flava (611)

X-RAY DIFFRACTION

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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	3.5 M Sodium formate, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.084	α = 90
b = 41.316	β = 99.815
c = 124.088	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 EIGER2 XE 16M		2023-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.166	122.272	92.5	0.081	0.034	0.989	7.2	6.2		98981

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.166	1.321	62.3		0.765	0.548	0.029	1.8	3.4

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	1.17	122.272	98972	4902	63.654	0.187	0.1861	0.186	0.2038	0.2038	15.705

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]
0.124		0.201	-0.27		0.072

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.751
r_dihedral_angle_2_deg	14.567
r_dihedral_angle_3_deg	11.051
r_dihedral_angle_1_deg	6.567
r_lrange_it	5.105
r_scangle_it	2.765
r_angle_refined_deg	1.976
r_scbond_it	1.847
r_mcangle_it	1.501
r_mcbond_it	0.971
r_nbtor_refined	0.316
r_xyhbond_nbd_refined	0.239
r_symmetry_nbd_refined	0.239
r_symmetry_xyhbond_nbd_refined	0.218
r_nbd_refined	0.214
r_chiral_restr	0.123
r_ncsr_local_group_1	0.082
r_gen_planes_refined	0.012
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3994
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
MOLREP	phasing