2DEJ

Crystal Structure of galaktokinase from Pyrococcus horikoshii with AMP-PN and galactose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	295	2.5% PEG 4000, 50mM magnesium chloride, 0.1M MES, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2	38.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.945	α = 90
b = 38.997	β = 109.6
c = 81.188	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	IMAGE PLATE	RIGAKU RAXIS V	mirrors	2005-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	1.0	SPring-8	BL26B1

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	1.45	30	98.5	0.077	14.4	3	54813	53991		-1.5

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)
	1.45	1.48	96.6		0.478	2.3	2.7	2642

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2CZ9	1.5	20	47224	47224	2535	98.7	0.191	0.18909	0.187	0.22807	RANDOM	15.952

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]
-0.43		-0.47	0.26		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.838
r_dihedral_angle_4_deg	14.614
r_dihedral_angle_3_deg	12.103
r_dihedral_angle_1_deg	5.985
r_scangle_it	3.344
r_scbond_it	2.209
r_mcangle_it	1.366
r_angle_refined_deg	1.294
r_mcbond_it	0.867
r_nbtor_refined	0.309
r_nbd_refined	0.194
r_symmetry_vdw_refined	0.179
r_symmetry_hbond_refined	0.14
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
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	2775
Nucleic Acid Atoms
Solvent Atoms	343
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
SCALEPACK	data scaling