6NDI | pdb_00006ndi

Crystal Structure of the Sugar Binding Domain of LacI Family Protein from Klebsiella pneumoniae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	Protein: 3.0 mg/ml, 0.01M Tris-HCl pH 8.3; Screen: Classics II (C1), 3.5M Sodium formate pH 7.0; Cryo: 4.0M Sodium formate.

Crystal Properties
Matthews coefficient	Solvent content
2.5	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.737	α = 90
b = 110.478	β = 97.94
c = 37.777	γ = 90

Symmetry
Space Group	C 1 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	CCD	MARMOSAIC 300 mm CCD	C(111)	2018-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.6	30	99.9	0.114	0.114	0.124	0.049	19.3	6.3		22623		-3	55.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	100		0.804	0.804	0.875	0.342	0.867	2.3	6.4

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.6	29.83	21591	1007	99.72	0.18447	0.18222	0.19	0.23513	0.24	RANDOM	58.782

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]
1.22		-0.7	-2.25		1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.468
r_dihedral_angle_4_deg	9.878
r_dihedral_angle_3_deg	8.988
r_long_range_B_refined	8.755
r_long_range_B_other	8.718
r_mcangle_it	4.756
r_mcangle_other	4.755
r_scangle_other	4.648
r_mcbond_it	2.764
r_mcbond_other	2.764
r_scbond_it	2.706
r_scbond_other	2.706
r_dihedral_angle_1_deg	1.888
r_angle_refined_deg	1.395
r_angle_other_deg	0.368
r_chiral_restr	0.066
r_gen_planes_refined	0.053
r_gen_planes_other	0.048
r_bond_refined_d	0.005
r_bond_other_d	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	4216
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing