3EK5 | pdb_00003ek5

Unique GTP-binding Pocket and Allostery of UMP Kinase from a Gram-Negative Phytopathogen Bacterium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EK6	PDB ENTRY 3EK6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	298	0.1M Na Citrate, 19.5% PEG 3350, 0.05M (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.634	α = 90
b = 119.638	β = 90
c = 125.18	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 210		2007-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13C1	0.97315	NSRRC	BL13C1

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	2.56	86.39	99.7	0.063	0.05	23.7	5.4	55638	55392	2	2

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	2.56	2.65	99.8		0.504	0.3	3.3	5

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	PDB ENTRY 3EK6	2.56	27.3	52509	2814	98.95	0.20858	0.20626	0.2	0.25157	0.25	RANDOM	55.136

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]
1.46			1.2		-2.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.421
r_dihedral_angle_4_deg	18.391
r_dihedral_angle_3_deg	17.823
r_dihedral_angle_1_deg	4.843
r_scangle_it	1.766
r_mcangle_it	1.755
r_angle_refined_deg	1.382
r_mcbond_it	1.041
r_scbond_it	1.025
r_symmetry_vdw_refined	0.361
r_nbtor_refined	0.33
r_nbd_refined	0.268
r_symmetry_hbond_refined	0.265
r_xyhbond_nbd_refined	0.219
r_chiral_restr	0.083
r_bond_refined_d	0.012
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	10785
Nucleic Acid Atoms
Solvent Atoms	507
Heterogen Atoms	192

Software

Software
Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling