1VM8 | pdb_00001vm8

Crystal structure of UDP-N-acetylglucosamine pyrophosphorylase (Agx2) from Mus musculus at 2.50 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	277	1.6M (NH4)2SO4, 0.1M Cacodylate pH 6.5, 0.2M NaCl , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.094	α = 90
b = 73.402	β = 99.83
c = 107.132	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	ADSC		2003-06-05	M	SINGLE WAVELENGTH
2	1	x-ray		M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1
2	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9792,1.0000,0.9791	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	29.11	99.3	0.073	9.5	3.4		42134			54.17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.5	2.64	96.9		0.402	2.7	3.3	5964

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.5	29.11	39990	2124	99.2	0.20971	0.20676	0.21	0.26573	0.27	RANDOM	41.392

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]
-2.11		-2.47	-2.7		3.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.707
r_dihedral_angle_3_deg	16.535
r_dihedral_angle_4_deg	16.483
r_dihedral_angle_1_deg	7.055
r_scangle_it	6.11
r_scbond_it	4.28
r_mcangle_it	2.513
r_mcbond_it	1.872
r_angle_refined_deg	1.417
r_angle_other_deg	0.794
r_mcbond_other	0.408
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.23
r_symmetry_vdw_other	0.207
r_nbtor_refined	0.188
r_nbd_other	0.182
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.161
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.076
r_chiral_restr	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7504
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	13

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling