7QJR | pdb_00007qjr

Crystal structure of cutinase 1 from Thermobifida fusca DSM44342 (703)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4CG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		281	20 % PEG 3350, 0.02 M sodium / potassium phosphate, 0.1 M Bis-Tris propane pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.68	α = 90
b = 71.68	β = 90
c = 102.52	γ = 120

Symmetry
Space Group	P 32 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 PILATUS3 6M		2020-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

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	1.51	62.08	100	0.115	0.027	0.999	14.5	19.4		48462

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	1.51	1.54	100		3.682	0.852	0.35	0.9

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	4CG1	1.51	62.077	48416	2307	99.996	0.156	0.1542	0.17	0.1855	0.19	25.381

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]
0.041	0.021		0.041		-0.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.004
r_dihedral_angle_4_deg	17.457
r_dihedral_angle_3_deg	11.068
r_dihedral_angle_1_deg	6.651
r_lrange_it	5.624
r_lrange_other	5.516
r_scangle_it	3.943
r_scangle_other	3.941
r_scbond_other	2.627
r_scbond_it	2.625
r_mcangle_it	2.431
r_mcangle_other	2.43
r_angle_refined_deg	2.044
r_mcbond_it	1.617
r_angle_other_deg	1.614
r_mcbond_other	1.608
r_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.19
r_xyhbond_nbd_refined	0.189
r_symmetry_nbd_other	0.182
r_nbd_other	0.18
r_symmetry_nbd_refined	0.179
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_other	0.108
r_chiral_restr	0.107
r_symmetry_nbtor_other	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2018
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	10

Software

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