3FBA | pdb_00003fba

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GX1	PDB ENTRY 1GX1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	0.2M potassium sodium tartate tetrahydrate, tri-sodium citrate dihydrate, pH5.6, 2.0M ammonium sulphate, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
7.1	80

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.127	α = 90
b = 144.127	β = 90
c = 144.127	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	CCD	ADSC Q210 2D	mirrors	2004-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9756	ESRF	ID29

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	3.1	29.42	99.9	0.101	0.101	6.188	12.2	9187	9178

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)
1	3.1	3.27	100		0.326	0.326	2.3	12.5	1318

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	PDB ENTRY 1GX1	3.1	24.72	9187	9160	436	99.91	0.187	0.187	0.186	0.1979	0.198	0.2097	RANDOM	55.168

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	34.953
r_dihedral_angle_3_deg	16.277
r_dihedral_angle_4_deg	15.927
r_dihedral_angle_1_deg	5.391
r_scangle_it	1.902
r_angle_refined_deg	1.612
r_scbond_it	1.136
r_mcangle_it	0.974
r_mcbond_it	0.547
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.953
r_dihedral_angle_3_deg	16.277
r_dihedral_angle_4_deg	15.927
r_dihedral_angle_1_deg	5.391
r_scangle_it	1.902
r_angle_refined_deg	1.612
r_scbond_it	1.136
r_mcangle_it	0.974
r_mcbond_it	0.547
r_nbtor_refined	0.307
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.211
r_xyhbond_nbd_refined	0.172
r_symmetry_hbond_refined	0.136
r_chiral_restr	0.118
r_bond_refined_d	0.013
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1183
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	47

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	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.