7TZP | pdb_00007tzp

Crystal Structure of Putataive Short-Chain Dehydrogenase/Reductase (FabG) from Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 in Complex with NADH

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	292	Protein: 13.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: ComPAS (A2), 0.5M Potassium chloride, 12% (w/v) PEGr800, 10% (w/v) Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.387	α = 90
b = 256.02	β = 90
c = 260.642	γ = 90

Symmetry
Space Group	F 2 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	MARMOSAIC 300 mm CCD	Be	2020-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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)	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	2.6	30	100	0.157	0.157	0.169	0.061	0.993	13.8	7.6		82427		-3	43

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		1.229	1.229	1.318	0.475	0.76	2	7.7

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	29.99	78066	4266	99.89	0.1911	0.1892	0.2	0.2266	0.23	RANDOM	49.129

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]
1.24			-0.57		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.657
r_dihedral_angle_3_deg	6.105
r_dihedral_angle_4_deg	5.518
r_angle_other_deg	2.226
r_dihedral_angle_1_deg	1.395
r_angle_refined_deg	1.175
r_chiral_restr	0.048
r_bond_other_d	0.035
r_gen_planes_other	0.006
r_gen_planes_refined	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.657
r_dihedral_angle_3_deg	6.105
r_dihedral_angle_4_deg	5.518
r_angle_other_deg	2.226
r_dihedral_angle_1_deg	1.395
r_angle_refined_deg	1.175
r_chiral_restr	0.048
r_bond_other_d	0.035
r_gen_planes_other	0.006
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14369
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms	344

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	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.