4YCO | pdb_00004yco

E. coli dihydrouridine synthase C (DusC) in complex with tRNAPhe

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BFA	4BFA, 3L0U
experimental model	PDB	3L0U	4BFA, 3L0U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	11% w/v PEG 6K, 100 mM HEPES, 200 mM MgCl2, 10 mM MnCl2,

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.585	α = 90
b = 176.895	β = 90
c = 238.413	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	PSI PILATUS 6M		2012-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97950	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.1	49.25	99.9	0.061	0.033	0.999	15.7	4.5		123558		-3	37.209

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	100		0.999	0.522	0.523	1.7	4.7	6073

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4BFA, 3L0U	2.1	49.21	122260	1241	99.87	0.1927	0.1924	0.1949	0.2234	0.2234	RANDOM	46.048

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]
-2.41			3.34		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.304
r_dihedral_angle_4_deg	19.125
r_dihedral_angle_3_deg	13.375
r_dihedral_angle_1_deg	5.932
r_angle_refined_deg	1.263
r_angle_other_deg	0.993
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7257
Nucleic Acid Atoms	4533
Solvent Atoms	495
Heterogen Atoms	240

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction