4GI7 | pdb_00004gi7

Crystal structure of Klebsiella pneumoniae pantothenate kinase in complex with a pantothenate analogue

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	0.5 uL protein + 0.5 uL buffer (20% PEG3350, 0.2 M tri-lithium citrate, pH 7.0) + 0.2 uL 40% 2,5-hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.928	α = 90
b = 130.938	β = 90
c = 193.022	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARMOSAIC 300 mm CCD		2012-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03321	APS	23-ID-B

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	40	99.86	0.129	9.2755	7.1	235112	234904

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	2.06	99.11		0.85		6.36	33760

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		THROUGHOUT	1.95	39.681	234630	11741	99.778	0.188	0.186	0.19	0.22	0.23	RANDOM	33.063

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]
-0.596			-0.639		1.236

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.055
r_dihedral_angle_4_deg	19.215
r_dihedral_angle_3_deg	13.616
r_dihedral_angle_1_deg	5.809
r_mcangle_it	3.144
r_mcbond_it	2.029
r_mcbond_other	2.029
r_angle_refined_deg	1.385
r_angle_other_deg	0.788
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.055
r_dihedral_angle_4_deg	19.215
r_dihedral_angle_3_deg	13.616
r_dihedral_angle_1_deg	5.809
r_mcangle_it	3.144
r_mcbond_it	2.029
r_mcbond_other	2.029
r_angle_refined_deg	1.385
r_angle_other_deg	0.788
r_chiral_restr	0.076
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19893
Nucleic Acid Atoms
Solvent Atoms	1023
Heterogen Atoms	371

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction

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.