7C9M | pdb_00007c9m

The structure of product-bound CntL, an aminobutyrate transferase in staphylopine biosynthesis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7C7M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.3 M Magnesium formate dihydrate, 26% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.519	α = 90
b = 96.684	β = 90
c = 211.428	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	PIXEL	DECTRIS PILATUS3 6M		2019-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	1.00000	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.7	50	96.8	0.065	0.998	31.9	6.2		34032

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	99.4		0.61	1.88	6.1

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	7C7M	2.7	49.9	32206	1680	96.83	0.24423	0.24204	0.24	0.285	0.28	RANDOM	82.731

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]
-0.61			3.46		-2.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.54
r_dihedral_angle_4_deg	13.9
r_dihedral_angle_3_deg	13.785
r_dihedral_angle_1_deg	4.862
r_long_range_B_refined	2.69
r_long_range_B_other	2.69
r_mcangle_it	1.204
r_mcangle_other	1.204
r_scangle_other	0.774
r_angle_refined_deg	0.771
r_angle_other_deg	0.699
r_mcbond_other	0.651
r_mcbond_it	0.65
r_scbond_it	0.422
r_scbond_other	0.422
r_chiral_restr	0.031
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7860
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	152

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing