2UYP

Crystal structure of E. coli TdcF with bound propionate

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QU9	PDB ENTRY 1QU9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		10% PEG 1000, 8% PEG 8000, NO BUFFER, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.02	46.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.435	α = 90
b = 85.744	β = 90
c = 62.512	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	OSMIC CONFOCAL MIRRORS	2002-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	2.45	25.25	98.9	0.08	12.49	3.4		14818			35.93

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	2.45	2.54	94		0.3	2.58

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 1QU9	2.44	24.58	14817	756	99.2	0.171	0.166	0.253	RANDOM	21.23

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]
-1.007			0.8		0.207

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.278
r_dihedral_angle_4_deg	22.264
r_dihedral_angle_3_deg	17.594
r_dihedral_angle_1_deg	7.077
r_scangle_it	4.329
r_scbond_it	2.766
r_angle_refined_deg	1.843
r_mcangle_it	1.79
r_mcbond_it	1.122
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.243
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.206
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.112
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	2860
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing