2Q6V

Crystal Structure of GumK in complex with UDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HY7	PDB entry 2HY7 Apo protein GumK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop and soaking of crystals in UDPGlcA 100 mM	8.2	293	0.1 M Tris-HCl, 35% (w/v) PEG 3350, 0.2 M Li2SO4, 0.1 M LiCl, pH 8.2, hanging drop and soaking of crystals in UDPGlcA 100 mM, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.99	69.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.21	α = 90
b = 121.21	β = 90
c = 170.724	γ = 120

Symmetry
Space Group	P 65 2 2

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	MARRESEARCH	beam focused by a cilindrically curved mirror	2006-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	1.427	NSLS	X12C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.28	104.971	98.5	0.104	0.104	4.3	10.1		33916

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.28	2.4	93.8		0.303	0.303	2.2	9.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	ARP/wARP	THROUGHOUT	PDB entry 2HY7 Apo protein GumK	2.28	104.83	32197	32197	1714	98.51	0.17746	0.17541	0.21641	RANDOM	21.077

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]
0.22	0.11		0.22		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.795
r_dihedral_angle_4_deg	19.678
r_dihedral_angle_3_deg	13.382
r_dihedral_angle_1_deg	8.549
r_scangle_it	4.371
r_scbond_it	2.812
r_angle_refined_deg	1.682
r_mcangle_it	1.639
r_mcbond_it	1.08
r_nbtor_refined	0.319
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.227
r_xyhbond_nbd_refined	0.206
r_symmetry_hbond_refined	0.194
r_chiral_restr	0.105
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
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	2935
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms	25

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
ARP/wARP	model building