3F1C | pdb_00003f1c

CRYSTAL STRUCTURE OF 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Listeria monocytogenes

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	294	100MM POTASSIUM THIOCYANATE, PH 7.5, 30% PEG MME2000, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.202	α = 90
b = 45.938	β = 108.89
c = 79.007	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	90	CCD	ADSC QUANTUM 315	MIRRORS	2008-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A		NSLS	X29A

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	2.3	50	98.2	0.074	7.4	3.8		24210		-5	56.31

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	2.3	2.38	100		0.605	1.5	3.8

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	SAD	THROUGHOUT	2.3	20	22869	764	98.22	0.24195	0.24075	0.24	0.27672	0.27	RANDOM	55.22

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]
1.53		0.24	-1.33		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.242
r_dihedral_angle_3_deg	18.638
r_dihedral_angle_4_deg	14.176
r_scangle_it	8.371
r_scbond_it	6.112
r_dihedral_angle_1_deg	5.891
r_mcangle_it	4.486
r_mcbond_it	2.841
r_angle_refined_deg	1.274
r_symmetry_hbond_refined	0.328
r_nbtor_refined	0.292
r_xyhbond_nbd_refined	0.183
r_nbd_refined	0.144
r_symmetry_vdw_refined	0.135
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3658
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms

Software

Software
Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing