1VK4 | pdb_00001vk4

Crystal structure of PfkB Carbohydrate kinase (TM0415) from Thermotoga maritima at 1.91 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7	277	TRIS pH 7, 15% Ethanol , pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.29	α = 90
b = 68.53	β = 90
c = 96.02	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 315		2004-04-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.939244, 0.979414, 0.979121	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.91	19.77	89.4	0.066	27.3	12.6		20420			27.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	2.02	58		0.209	9.4	8.1	1885

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.91	19.77	19333	1038	89.4	0.17007	0.1676	0.18	0.21938	0.23	RANDOM	20.243

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]
0.27			-0.72		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	8.508
r_dihedral_angle_1_deg	6.17
r_scbond_it	5.713
r_mcangle_it	3.663
r_mcbond_it	2.074
r_angle_refined_deg	1.542
r_angle_other_deg	0.873
r_symmetry_vdw_other	0.31
r_nbd_other	0.244
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.16
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.101
r_chiral_restr	0.097
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2212
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
XDS	data scaling
SHELX	model building
autoSHARP	phasing
REFMAC	refinement
CCP4	data scaling
SHELX	phasing