2PX7

Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Thermus thermophilus HB8

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YE7	PDB entry 1YE7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (6.36 mg/ml) AND RESERVOIR SOLUTION CONTAINING 0.9M Li Sulfate, 0.09M HEPES pH 8.0, 0.01M Betaine, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.084	α = 90
b = 104.084	β = 90
c = 107.76	γ = 120

Symmetry
Space Group	P 61

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	RIGAKU JUPITER 210		2007-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.00000	SPring-8	BL26B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.2	50	100	0.043	25.6	11		33616

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.28	100		0.286		11	3339

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1YE7	2.2	50	33570	1699	99.94	0.228	0.227	0.248	RANDOM	37.878

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]
1.05	0.53		1.05		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.015
r_dihedral_angle_4_deg	20.604
r_dihedral_angle_3_deg	15.689
r_dihedral_angle_1_deg	8.895
r_scangle_it	3.451
r_scbond_it	2.048
r_angle_refined_deg	1.467
r_mcangle_it	1.426
r_mcbond_it	0.775
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.015
r_dihedral_angle_4_deg	20.604
r_dihedral_angle_3_deg	15.689
r_dihedral_angle_1_deg	8.895
r_scangle_it	3.451
r_scbond_it	2.048
r_angle_refined_deg	1.467
r_mcangle_it	1.426
r_mcbond_it	0.775
r_nbtor_refined	0.302
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.215
r_xyhbond_nbd_refined	0.168
r_symmetry_vdw_refined	0.167
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3006
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	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.