8ZX0 | pdb_00008zx0

Crystal Structure of CntL in complex with a dual-site inhibitor

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		289	0.23 M Calcium acetate, 0.1 M Sodium cacodylate 6.4, 35% PEG 300, 1.5% iBu

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.395	α = 90
b = 135.511	β = 90
c = 131.814	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER X 16M		2021-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97914	SSRF	BL17U1

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	2.09	67.76	97.1	0.072	0.998	9.5	5.1		29426

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.2	100		0.853	0.668		5.4

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	2.091	67.756	29384	1475	96.974	0.203	0.2014	0.2056	0.2393	0.239	41.628

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]
3.585			-2.244		-1.342

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.447
r_dihedral_angle_6_deg	15.2
r_dihedral_angle_2_deg	8.154
r_lrange_it	6.859
r_lrange_other	6.846
r_dihedral_angle_1_deg	5.623
r_scangle_it	4.382
r_scangle_other	4.381
r_mcangle_other	2.908
r_mcangle_it	2.906
r_scbond_it	2.775
r_scbond_other	2.774
r_mcbond_it	1.85
r_mcbond_other	1.85
r_angle_refined_deg	1.175
r_angle_other_deg	0.418
r_symmetry_nbd_refined	0.232
r_nbd_other	0.209
r_nbd_refined	0.208
r_symmetry_nbd_other	0.202
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.131
r_symmetry_metal_ion_refined	0.09
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_other	0.029
r_metal_ion_refined	0.013
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3701
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	97

Software

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