3EOR

Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	0.5M ammonium sulphate, tri-sodium citrate, lithium sulphate monohydrate, pH 5.6, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
7.329383	83.218231

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.681	α = 90
b = 145.681	β = 90
c = 145.681	γ = 90

Symmetry
Space Group	I 21 3

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	RIGAKU RAXIS IV++	mirrors	2003-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.801	29.737	99.9	0.087	0.087	6.561	14.5	12830	12818		5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.95	100		0.476	0.476	1.6	14.8	1843

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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	2.9	24.98	5	12818	11538	557	99.93	0.189	0.188	0.209	RANDOM	57.048

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.754
r_dihedral_angle_4_deg	21.8
r_dihedral_angle_3_deg	16.655
r_dihedral_angle_1_deg	9.234
r_scangle_it	8.508
r_scbond_it	5.158
r_mcangle_it	3.283
r_angle_refined_deg	2.329
r_mcbond_it	1.918
r_symmetry_hbond_refined	0.538

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.754
r_dihedral_angle_4_deg	21.8
r_dihedral_angle_3_deg	16.655
r_dihedral_angle_1_deg	9.234
r_scangle_it	8.508
r_scbond_it	5.158
r_mcangle_it	3.283
r_angle_refined_deg	2.329
r_mcbond_it	1.918
r_symmetry_hbond_refined	0.538
r_nbtor_refined	0.345
r_nbd_refined	0.285
r_symmetry_vdw_refined	0.284
r_xyhbond_nbd_refined	0.202
r_chiral_restr	0.169
r_bond_refined_d	0.029
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1175
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms	40

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

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.