2Y6P

Evidence for a Two-Metal-Ion-Mechanism in the Kdo- Cytidylyltransferase KdsB

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		THE DROPS CONTAINED EQUAL AMOUNTS OF KDSB (10 MG/ML IN 20 MM TRIS-HCL, PH 7.5, 100 MM NACL, 5 MM MGCL2, 2 MM 2-MERCAPTOETHANOL, SUPPLEMENTED WITH 1 MM CTP) AND RESERVOIR SOLUTION (0.1 M HEPES PH 7.5, 18.8% ISOPROPANOL, 18.7% PEG 4000).

Crystal Properties
Matthews coefficient	Solvent content
2.57	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.175	α = 90
b = 51.175	β = 102.68
c = 107.514	γ = 90

Symmetry
Space Group	C 1 2 1

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 SX-165	MIRRORS	2003-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13		EMBL/DESY, HAMBURG	X13

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	2.1	29.36	94.8	0.04	16.74	3.75		46213			31.9

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	2.1	2.18	88.5		0.12	6.12

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	MIRAS	THROUGHOUT	NONE	2.1	29.35	42413	2263	91.48	0.21369	0.21129	0.25792	RANDOM	40.206

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]
0.3		1.8	0.78		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.024
r_dihedral_angle_4_deg	18.491
r_dihedral_angle_3_deg	17.106
r_dihedral_angle_1_deg	5.931
r_scangle_it	3.1
r_scbond_it	1.816
r_angle_refined_deg	1.375
r_mcangle_it	1.039
r_mcbond_it	0.543
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	5673
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	105

Software

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