2XF8

Structure of the D-Erythrose-4-Phosphate Dehydrogenase from E. coli in complex with a NAD cofactor analog (3-Chloroacetyl adenine pyridine dinucleotide) and sulfate anion

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X5J	PDB ENTRY 2X5J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		20 % (W/V) PEG 2000 MME, 100 MM TRIS-HCL BUFFER PH 8.5, 200 MM LI2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.57	51.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.18	α = 91.3
b = 111.66	β = 96.11
c = 135.47	γ = 88.44

Symmetry
Space Group	P 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	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.95	48.7	95.4	0.09	10.1	2.1		112592

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	2.95	3.03	95.8		0.49	2	2

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 2X5J	2.95	48.72	106962	5630	100	0.23904	0.23688	0.27981	RANDOM	38.162

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]
4.95	-2.66	-2.68	-2.48	-0.83	-2.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.639
r_dihedral_angle_4_deg	19.064
r_dihedral_angle_3_deg	18.744
r_dihedral_angle_1_deg	6.109
r_scangle_it	1.995
r_angle_other_deg	1.825
r_angle_refined_deg	1.691
r_scbond_it	1.087
r_mcangle_it	0.906
r_mcbond_it	0.471
r_chiral_restr	0.063
r_mcbond_other	0.059
r_bond_refined_d	0.013
r_bond_other_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	39641
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms	432

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing