4WGH | pdb_00004wgh

Crystal structure of aldo/keto reductase from Klebsiella pneumoniae in complex with NADP and acetate at 1.8 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	289	0.45 ul of 13 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP and 30mM NADP were mixed with 0.45 ul of 2.8 M Sodium Acetate pH 6.2 and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci).

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.483	α = 90
b = 99.483	β = 90
c = 55.181	γ = 120

Symmetry
Space Group	P 62

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 225 mm CCD	Beryllium Lenses	2014-03-20	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)	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	1.8	50	99.1	0.048	0.056	0.028	10.2	3.9		56317		-3	28.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	97.3		0.62	0.723	0.369	0.726	1.43	3.7	2809

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	1.8	50	27524	1473	99.87	0.1466	0.1446	0.15	0.1854	0.19	RANDOM	38.07

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]
-1.17	-0.59		-1.17		3.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.649
r_dihedral_angle_4_deg	17.887
r_dihedral_angle_3_deg	14.033
r_dihedral_angle_1_deg	5.831
r_angle_refined_deg	1.654
r_mcangle_it	1.51
r_mcbond_it	1.02
r_mcbond_other	1.012
r_angle_other_deg	0.846
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.649
r_dihedral_angle_4_deg	17.887
r_dihedral_angle_3_deg	14.033
r_dihedral_angle_1_deg	5.831
r_angle_refined_deg	1.654
r_mcangle_it	1.51
r_mcbond_it	1.02
r_mcbond_other	1.012
r_angle_other_deg	0.846
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2166
Nucleic Acid Atoms
Solvent Atoms	227
Heterogen Atoms	52

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
DM	phasing
MLPHARE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

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.