3GE1 | pdb_00003ge1

2.7 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with ADP and Glycerol

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	295	2% Glycerol, PEG3350 20%, 0.2M Sodium dihydrogen Phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.412	α = 90
b = 193.651	β = 106.01
c = 91.844	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 300 mm CCD	BERYLLIUM LENSES	2008-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D		APS	21-ID-D

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	2.7	30	97.2	0.116	18.9	7.5		56438		-3	57.4

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	2.7	2.8	83.1		0.583	2.6	6.4

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 (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	3EZW	2.7	30	53455	53455	2855	96.8	0.194	0.191	0.21	0.253	0.27	RANDOM	32.81

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]
12.01		2.84	-6.79		-3.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.653
r_dihedral_angle_4_deg	14.684
r_dihedral_angle_3_deg	11.141
r_scangle_it	4.516
r_scbond_it	2.862
r_dihedral_angle_1_deg	2.273
r_mcangle_it	1.593
r_angle_refined_deg	1.011
r_mcbond_it	0.848
r_angle_other_deg	0.691
r_mcbond_other	0.247
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15660
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	176

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling