2R3B | pdb_00002r3b

CRYSTAL STRUCTURE OF a ribokinase-like superfamily protein (EF1790) FROM ENTEROCOCCUS FAECALIS V583 AT 1.80 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 0.2M MgCl2, 10.0% PEG 3000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.817	α = 90
b = 159.564	β = 90
c = 102.497	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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-06-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97926, 0.97895	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	29.591	99.4	0.102	0.102	6.2	5		73792			20.819

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	1.8	1.85	98.9		0.67	0.67	1.1	5.1	5365

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 (All)	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	MAD	THROUGHOUT	1.8	29.591	73782	3709	99.28	0.152	0.152	0.15	0.16	0.183	0.19	RANDOM	18.233

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]
1.35			-0.98		-0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.183
r_dihedral_angle_3_deg	12.507
r_dihedral_angle_4_deg	10.392
r_scangle_it	6.791
r_dihedral_angle_1_deg	5.551
r_scbond_it	4.87
r_mcangle_it	3.008
r_mcbond_it	1.974
r_angle_refined_deg	1.459
r_angle_other_deg	0.925
r_mcbond_other	0.617
r_symmetry_vdw_other	0.282
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.202
r_symmetry_hbond_refined	0.188
r_nbd_other	0.184
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.089
r_nbtor_other	0.087
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4327
Nucleic Acid Atoms
Solvent Atoms	621
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHARP	phasing
SHELXD	phasing