2YQC

Crystal Structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the apo-like form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JVD	PDB ENTRY 1JVD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	30% PEG 6000, 0.1M ammonium sulfate, 5% glycerol, 0.001M N-acetylglucosamine-1-phosphate, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.774	α = 90
b = 62.891	β = 97.82
c = 90.602	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	95	CCD	ADSC QUANTUM 210		2003-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

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	1.9	50	90.2	0.111	11.6	3.5		40383			17.8

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	1.9	1.97	68.4		0.337	2.6	2.5	3729

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JVD	1.9	39.7	41523	2055	99.2	0.174	0.174	0.201	RANDOM	24.3

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]
2.98		-0.4	-0.86		-2.12

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.2
c_scangle_it	3.51
c_scbond_it	2.47
c_mcangle_it	2.11
c_mcbond_it	1.47
c_angle_deg	1.4
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3720
Nucleic Acid Atoms
Solvent Atoms	436
Heterogen Atoms	7

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing