2R8E

Crystal structure of YrbI from Escherichia coli in complex with Mg

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.877	α = 118.84
b = 83.005	β = 118.77
c = 85.864	γ = 90.06

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		CCD	MARMOSAIC 225 mm CCD		2007-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97869	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	40					313166

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.4	29.34	296631	15726	94.72	0.1601	0.1586	0.18807	RANDOM	21.281

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]
-0.05	-0.08	-0.2	0.11	-0.02	-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.304
r_dihedral_angle_4_deg	17.278
r_dihedral_angle_3_deg	12.925
r_dihedral_angle_1_deg	6.257
r_sphericity_free	4.393
r_sphericity_bonded	4.045
r_scangle_it	3.622
r_scbond_it	2.688
r_rigid_bond_restr	1.845
r_mcangle_it	1.673
r_angle_refined_deg	1.368
r_mcbond_it	1.11
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.207
r_chiral_restr	0.134
r_symmetry_hbond_refined	0.11
r_bond_refined_d	0.01
r_metal_ion_refined	0.008
r_gen_planes_refined	0.006
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10564
Nucleic Acid Atoms
Solvent Atoms	2232
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement