7CWQ | pdb_00007cwq

Crystal structure of a novel cutinase from Burkhoderiales bacterium RIFCSPLOWO2_02_FULL_57_36

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5XFY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	Polyethylene Glycol 6000, Glycerol, MES

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.967	α = 90
b = 69.967	β = 90
c = 381.89	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	RAYONIX MX-300		2019-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

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	1.65	25	100	0.211	0.214	0.11	3.3	30.3		68361

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.71	100		0.779		13.5

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	5XFY	1.65	24.89	64801	3381	99.83	0.1663	0.1648	0.18	0.1955	0.2	RANDOM	14.978

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]
-0.11	-0.06		-0.11		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.337
r_dihedral_angle_4_deg	19.546
r_dihedral_angle_3_deg	12.34
r_dihedral_angle_1_deg	6.745
r_angle_refined_deg	1.491
r_angle_other_deg	1.471
r_chiral_restr	0.086
r_gen_planes_refined	0.012
r_bond_refined_d	0.01
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.337
r_dihedral_angle_4_deg	19.546
r_dihedral_angle_3_deg	12.34
r_dihedral_angle_1_deg	6.745
r_angle_refined_deg	1.491
r_angle_other_deg	1.471
r_chiral_restr	0.086
r_gen_planes_refined	0.012
r_bond_refined_d	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4074
Nucleic Acid Atoms
Solvent Atoms	530
Heterogen Atoms	20

Software

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

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.