3KHI

Crystal structure of a Putative Metal-dependent Hydrolase (YP_001336084.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.95 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	10.0000% polyethylene glycol 6000, 1.0000M lithium chloride, 0.1M Bicine pH 9.0, 0.001 M zinc chloride, 0.001 M Leucine-Chloromethyl ketone, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.19	α = 90
b = 131.19	β = 90
c = 37.12	γ = 90

Symmetry
Space Group	P 41 21 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 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	46.374	99.8	0.071	14.52			24283		-3	36.556

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	1.95	2.04	99.8		0.977	2.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.95	46.374	24240	1244	99.87	0.184	0.183	0.213	RANDOM	30.899

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]
0.15			0.15		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.65
r_dihedral_angle_4_deg	21.485
r_dihedral_angle_3_deg	12.096
r_scangle_it	6.735
r_dihedral_angle_1_deg	5.153
r_scbond_it	4.836
r_mcangle_it	2.93
r_mcbond_it	1.728
r_angle_refined_deg	1.276
r_angle_other_deg	0.918

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.65
r_dihedral_angle_4_deg	21.485
r_dihedral_angle_3_deg	12.096
r_scangle_it	6.735
r_dihedral_angle_1_deg	5.153
r_scbond_it	4.836
r_mcangle_it	2.93
r_mcbond_it	1.728
r_angle_refined_deg	1.276
r_angle_other_deg	0.918
r_mcbond_other	0.39
r_chiral_restr	0.074
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1737
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.