7QJP | pdb_00007qjp

Crystal structure of a cutinase enzyme from Saccharopolyspora flava (611)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JFR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20 % PEG 3350, 0.2 M sodium fluoride, 0.1 M Bis-Tris propane pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.336	α = 90
b = 89.336	β = 90
c = 74.324	γ = 120

Symmetry
Space Group	P 3 2 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		2021-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.8153	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	1.561	77.367	94.9	0.14	0.034	0.999	12.5	17.4		40562

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	1.561	1.652			2.153	0.548	0.632	1.4

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	1jfr	1.561	77.367	40562	1981	82.749	0.142	0.1406	0.15	0.1653	0.18	21.693

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]
0.013	0.007		0.013		-0.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.092
r_dihedral_angle_3_deg	11.036
r_dihedral_angle_4_deg	8.956
r_dihedral_angle_1_deg	6.804
r_lrange_it	5.877
r_lrange_other	5.576
r_scangle_it	2.738
r_scangle_other	2.737
r_angle_refined_deg	2.013
r_scbond_it	1.886
r_scbond_other	1.885
r_mcangle_other	1.768
r_mcangle_it	1.761
r_angle_other_deg	1.617
r_mcbond_it	1.17
r_mcbond_other	1.118
r_symmetry_xyhbond_nbd_other	0.555
r_symmetry_xyhbond_nbd_refined	0.277
r_symmetry_nbd_refined	0.253
r_xyhbond_nbd_refined	0.237
r_nbd_refined	0.223
r_symmetry_nbd_other	0.181
r_nbd_other	0.178
r_nbtor_refined	0.175
r_chiral_restr	0.108
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1949
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	13

Software

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