2IJ9 | pdb_00002ij9

Crystal Structure of Uridylate Kinase from Archaeoglobus Fulgidus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BRX	PDB entry 2BRX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	294	100MM SODIUM CITRATE, PH 4.5, 3.5M AMMONIUM SULFATE, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
4.32	71.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.277	α = 90
b = 94.277	β = 90
c = 186.672	γ = 90

Symmetry
Space Group	P 43 2 2

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	2006-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

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	2.6	50	87.6	0.093	0.081	6.3	6	23600	23600

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	2.6	2.69	54.5		0.502	0.78	0.5	1.4	1438

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entry 2BRX	2.9	20	17774	17774	595	95.09	0.28428	0.2828	0.28	0.33021	0.33	RANDOM	96.22

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]
2.73			2.73		-5.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.073
r_scangle_it	24.823
r_dihedral_angle_3_deg	19.465
r_dihedral_angle_4_deg	19.132
r_scbond_it	17.963
r_mcangle_it	12.32
r_mcbond_it	8.564
r_dihedral_angle_1_deg	7.897
r_angle_refined_deg	1.377
r_nbtor_refined	0.317
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_refined	0.172
r_symmetry_hbond_refined	0.16
r_chiral_restr	0.099
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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_refined
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3224
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
MOLREP	phasing