3BHR | pdb_00003bhr

E. coli TS complexed with 5-NO2dUMP and tetrahydrofolate at 1.9 A resolution (space group 152)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	2.5 M ammonium sulfate, 20 mM KH2PO4, 4MM DTT, 4MM 5-NO2dUMP, 4MM MTF, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.95	α = 90
b = 71.95	β = 90
c = 115.47	γ = 120

Symmetry
Space Group	P 31 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	293	DIFFRACTOMETER	ENRAF-NONIUS FAST		1996-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	1.5418

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	1.9	62.02	99	0.66	11.1	4	25412	25412

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	1.9	10	23761	1278	89.63	0.1684	0.16663	0.1715	0.20132	0.1983	RANDOM	21.933

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]
0.56	0.28		0.56		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.684
r_dihedral_angle_4_deg	23.346
r_dihedral_angle_3_deg	14.555
r_dihedral_angle_1_deg	6.301
r_scangle_it	4.463
r_scbond_it	2.787
r_angle_refined_deg	1.812
r_mcangle_it	1.776
r_angle_other_deg	1.582
r_mcbond_it	0.935
r_symmetry_vdw_other	0.294
r_mcbond_other	0.249
r_chiral_restr	0.248
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.144
r_symmetry_vdw_refined	0.141
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2153
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
MADNESS	data collection
PROCOR	data reduction
PROCOR	data scaling