1INI | pdb_00001ini

CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1I52	PDB ENTRY 1I52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	279	PEG 8000, CALCIUM ACETATE, MAGNESIUM CHLORIDE, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.99	α = 90
b = 46.764	β = 92.64
c = 38.387	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)	2001-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.773	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	90	98.6	0.026	0.026	26.4	2.8	20268	20268	1	1	21.6

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)
1	1.81	1.83	98.6		0.308	2.7	2.9	641

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1I52	1.82	44	17144	17144	866	82.9	0.222	0.222	0.21	0.273	0.27	RANDOM	36.2

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]
-7.95		-1.83	5		2.95

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.3
c_scangle_it	5.84
c_scbond_it	4.64
c_mcangle_it	4.3
c_mcbond_it	3.3
c_angle_deg	1.4
c_improper_angle_d	0.89
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1716
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

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.