3Q8H | pdb_00003q8h

Crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KE1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	289	27 mg/mL protein in 20% PEG 4000, 100 mM Tris, 200 mM NaCl. Crystals soaked in same conditions with 20 mM ligand and 5 mM ZnCl2 for 3 weeks. , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.69	α = 90
b = 67.76	β = 96.02
c = 60.02	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+		2010-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

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	1.75	19.9	98.8	0.025	27.83			46878		-3	25.962

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	1.75	1.8	92.7		0.176	4.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3ke1	1.75	19.9	46844	2359	98.85	0.1564	0.1549	0.17	0.1841	0.2	RANDOM	22.1886

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]
-0.01			0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.052
r_dihedral_angle_4_deg	17.371
r_dihedral_angle_3_deg	12.895
r_dihedral_angle_1_deg	5.373
r_scangle_it	3.415
r_scbond_it	2.152
r_angle_refined_deg	1.884
r_mcangle_it	1.374
r_mcbond_it	0.814
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.052
r_dihedral_angle_4_deg	17.371
r_dihedral_angle_3_deg	12.895
r_dihedral_angle_1_deg	5.373
r_scangle_it	3.415
r_scbond_it	2.152
r_angle_refined_deg	1.884
r_mcangle_it	1.374
r_mcbond_it	0.814
r_chiral_restr	0.108
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3420
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	93

Software

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

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.