2AMT

Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GX1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	290	0.1M ammonium sulfate, 10% PEG 200 MME, 0.1M sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.68	53.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.033	α = 90
b = 115.269	β = 90.18
c = 87.609	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 210	mirror	2004-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9756	ESRF	ID29

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	2.3	29.5	99.4	0.097	10.1	3.5	47682	47420		3.9	29.85

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)
	2.3	2.42	99.7		0.272	3.9	3.6	6904

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GX1	2.3	29.5	47682	45024	2397	99.5	0.2582	0.24516	0.24327	0.27952	RANDOM	32.618

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]
-3.19		0.24	6.86		-3.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.718
r_dihedral_angle_3_deg	14.84
r_dihedral_angle_4_deg	14.666
r_dihedral_angle_1_deg	4.979
r_angle_refined_deg	0.998
r_scangle_it	0.968
r_mcangle_it	0.594
r_scbond_it	0.518
r_mcbond_it	0.336
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.718
r_dihedral_angle_3_deg	14.84
r_dihedral_angle_4_deg	14.666
r_dihedral_angle_1_deg	4.979
r_angle_refined_deg	0.998
r_scangle_it	0.968
r_mcangle_it	0.594
r_scbond_it	0.518
r_mcbond_it	0.336
r_nbtor_refined	0.294
r_symmetry_vdw_refined	0.182
r_nbd_refined	0.173
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.06
r_metal_ion_refined	0.054
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6996
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	266

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	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.