3JVH

Crystal structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with FOL fragment 8395

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F0D	pdb entry 3F0D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	289	20% PEG 3350, 0.2 M magnesium formate, 34.4 mg/mL protein, 0.4/0.4 uL drops, 20 mM fragment 8395, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.12	α = 90
b = 67.65	β = 96.32
c = 60	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	CCD	RIGAKU SATURN 944+		2009-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.69	50	97.3	0.033	26.57			50817		-3	26.268

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	1.69	1.73	82.8		0.35	2.7		3188

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	pdb entry 3F0D	1.69	19.5	50816	2590	97.42	0.169	0.167	0.195	RANDOM	14.092

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]
-0.09		0.01	0.06		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.087
r_dihedral_angle_4_deg	17.681
r_dihedral_angle_3_deg	12.765
r_dihedral_angle_1_deg	5.011
r_scangle_it	2.511
r_scbond_it	1.544
r_angle_refined_deg	1.293
r_mcangle_it	1.028
r_mcbond_it	0.581
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.087
r_dihedral_angle_4_deg	17.681
r_dihedral_angle_3_deg	12.765
r_dihedral_angle_1_deg	5.011
r_scangle_it	2.511
r_scbond_it	1.544
r_angle_refined_deg	1.293
r_mcangle_it	1.028
r_mcbond_it	0.581
r_chiral_restr	0.076
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3406
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	57

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.