1UEK | pdb_00001uek

Crystal structure of 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	sodium acetate, isopropanol, butanol, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.603	α = 90
b = 66.21	β = 90
c = 76.4	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	MARRESEARCH		2002-12-10	M	MAD
2	1	x-ray	100	CCD	MARRESEARCH		2002-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	0.9709, 0.9794, 0.9799, 0.9822	SPring-8	BL44B2
2	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	0.9794	SPring-8	BL44B2

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	1.7	20	93.3	0.072	9.2	3.7	80882	95700

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)
	1.7	1.76			0.264

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.7	19.57	26111	24710	1252	94.6	0.18419	0.18248	0.21796	0.1964	RANDOM	20.251

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]
0.56			-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.99
r_scangle_it	4.714
r_scbond_it	2.803
r_mcangle_it	1.681
r_angle_refined_deg	1.501
r_mcbond_it	0.914
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.185
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.113
r_symmetry_hbond_refined	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2032
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing