4JJP

2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	protein: 3.7 mg/mL crystallization: 30% Jeffamine ED-2001, 0.1 M HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.79	31.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.751	α = 90
b = 79.741	β = 90
c = 92.863	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	Be-Lenses	2013-02-09	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)	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	2.05	30	99.9	0.077	21.7	6	26751	26751		-3	33

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	2.05	2.09	99.8		0.575	3.1	5.9	1321

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UB0	2.056	28.86	25359	25359	1345	99.34	0.18305	0.18123	0.21809	RANDOM	35.432

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]
-3.24			-0.77		4.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.322
r_dihedral_angle_4_deg	13.858
r_dihedral_angle_3_deg	10.474
r_scangle_it	3.781
r_dihedral_angle_1_deg	3.521
r_scbond_it	2.279
r_angle_refined_deg	1.571
r_mcangle_it	1.395
r_angle_other_deg	0.917
r_mcbond_it	0.764

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.322
r_dihedral_angle_4_deg	13.858
r_dihedral_angle_3_deg	10.474
r_scangle_it	3.781
r_dihedral_angle_1_deg	3.521
r_scbond_it	2.279
r_angle_refined_deg	1.571
r_mcangle_it	1.395
r_angle_other_deg	0.917
r_mcbond_it	0.764
r_mcbond_other	0.196
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3427
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	15

Software

Software
Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.