2DEI

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CZ9	PDB ENTRY 2CZ9

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
2.02	39.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.333	α = 90
b = 39.067	β = 109.5
c = 81.418	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	2005-06-26	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	1.7	30	98.9	0.086	12.7	3	34628	34247		-1

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)
	1.7	1.74	99.3		0.364	3.2	3.1	2438

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2CZ9	1.7	15	32846	32846	1731	98.76	0.181	0.17897	0.17672	0.18	0.22132	0.22	RANDOM	14.432

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]
-0.56		-0.3	0.14		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.326
r_dihedral_angle_4_deg	16.432
r_dihedral_angle_3_deg	12.87
r_dihedral_angle_1_deg	5.792
r_scangle_it	3.875
r_scbond_it	2.488
r_mcangle_it	1.451
r_angle_refined_deg	1.395
r_mcbond_it	0.953
r_nbtor_refined	0.313
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.172
r_symmetry_hbond_refined	0.143
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.094
r_metal_ion_refined	0.017
r_bond_refined_d	0.011
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_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	2816
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	44

Software

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