3F0F | pdb_00003f0f

Co-crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with hydrolyzed CDP

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, SITTING DROP		289	34.4 mg/mL protein, Crystal ID 200564d9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.078	α = 90
b = 66.457	β = 90
c = 131.465	γ = 90

Symmetry
Space Group	P 21 21 21

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		2008-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	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	2.09	65.8	98.8	0.098	15.889	5.1		27899

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	2.09	2.18	98.4		0.549	2.5	4.3	2729

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	pdb entry 3F0D	2.09	50	27759	1406	98.35	0.2	0.197	0.19	0.246	0.24	RANDOM	31.043

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]
0.49			-0.01		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.18
r_dihedral_angle_4_deg	13.916
r_dihedral_angle_3_deg	13.684
r_dihedral_angle_1_deg	4.962
r_scangle_it	1.811
r_scbond_it	1.097
r_angle_refined_deg	1.048
r_mcangle_it	0.847
r_mcbond_it	0.461
r_chiral_restr	0.068

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.18
r_dihedral_angle_4_deg	13.916
r_dihedral_angle_3_deg	13.684
r_dihedral_angle_1_deg	4.962
r_scangle_it	1.811
r_scbond_it	1.097
r_angle_refined_deg	1.048
r_mcangle_it	0.847
r_mcbond_it	0.461
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3508
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	31

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	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.