1PT7

Crystal structure of the apo-form of the yfdW gene product of E. coli

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	298	Ammonium phosphate, sodium hepes, pH 7.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.921	α = 90
b = 118.634	β = 90
c = 136.305	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH	Mirrors	2002-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.98	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	20	98.3	0.048	9.8	4	85290	85290	2	2

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	1.7	1.79	97.2		0.268	0.268	2.8	3.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.8	20	2	85290	80019	2468	89.52	0.1598	0.15985	0.15889	0.19084	RANDOM	19.157

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]
2.05			-0.15		-1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.26
r_scangle_it	4.25
r_scbond_it	2.836
r_angle_refined_deg	1.749
r_mcangle_it	1.702
r_mcbond_it	1.028
r_angle_other_deg	0.916
r_symmetry_hbond_refined	0.532
r_nbd_other	0.249
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.172
r_symmetry_vdw_other	0.171
r_symmetry_vdw_refined	0.138
r_chiral_restr	0.114
r_nbtor_other	0.088
r_bond_refined_d	0.021
r_gen_planes_refined	0.01
r_gen_planes_other	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6432
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
SOLVE	phasing