3GHZ | pdb_00003ghz

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium

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, SITTING DROP	7.5	289	0.2 M Magnesium acetate,20% PEG-3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.974	α = 90
b = 143.974	β = 90
c = 143.974	γ = 90

Symmetry
Space Group	I 2 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	CCD	ADSC QUANTUM 315		2008-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	2.03	46	100	0.073	51.494	14.3	32255	32255			50.5

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	2.03	2.07	100		0.801	2.05	4.8	1607

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GX1	2.03	46	32219	32219	1632	99.94	0.168	0.168	0.166	0.18	0.205	0.21	RANDOM	32.007

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	36.835
r_dihedral_angle_4_deg	20.076
r_dihedral_angle_3_deg	16.83
r_dihedral_angle_1_deg	5.386
r_scangle_it	3.896
r_scbond_it	2.573
r_angle_refined_deg	1.644
r_mcangle_it	1.428
r_angle_other_deg	0.935
r_mcbond_it	0.855

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.835
r_dihedral_angle_4_deg	20.076
r_dihedral_angle_3_deg	16.83
r_dihedral_angle_1_deg	5.386
r_scangle_it	3.896
r_scbond_it	2.573
r_angle_refined_deg	1.644
r_mcangle_it	1.428
r_angle_other_deg	0.935
r_mcbond_it	0.855
r_mcbond_other	0.26
r_chiral_restr	0.101
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3475
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	25

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
MOLREP	phasing
HKL-3000	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.