4C23 | pdb_00004c23

L-fuculose kinase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CGK	PDB ENTRY 2CGK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2		SPFCSK AT A CONCENTRATION OF 24 MG ML-1, BUFFERED IN 20 MM TRIS-HCL (PH 7.2), 150 MM NACL, 1 MM MANGANESE CHLORIDE, AND 1 MM DTT WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES WITH A SOLUTION CONSISTING OF 4% (V PER V) ETHYLENE-GLYCOL, 100 MM 4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID (PH 7.5), AND 1.50 M AMMONIUM SULPHATE

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.624	α = 90
b = 60.624	β = 90
c = 280.013	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	RH COATED	2012-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2		SSRL	BL12-2

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	37	99.6	0.05	20.5	6.4		67536

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	2.11	100		0.16	9.2	6.9

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 2CGK	2	36.98	63900	3418	99.4	0.16863	0.16608	0.18	0.21597	0.23	RANDOM	31.896

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]
-3.71			-3.71		7.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.917
r_dihedral_angle_4_deg	19.136
r_dihedral_angle_3_deg	16.913
r_dihedral_angle_1_deg	6.812
r_mcangle_it	3.052
r_scbond_it	2.481
r_mcbond_it	2.07
r_angle_refined_deg	1.633
r_chiral_restr	0.105
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_it
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	7442
Nucleic Acid Atoms
Solvent Atoms	471
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing