1MFZ | pdb_00001mfz

Partially refined 2.8 A Crystal structure of GDP-mannose dehydrogenase from P. aeruginosa

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6		10% PEG 3350, 20% isopropanol, 0.1 M Na citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.173	α = 90
b = 136.834	β = 90
c = 218.562	γ = 90

Symmetry
Space Group	C 2 2 21

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 IV	Osmic confocal		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.8	94.691	98.7	0.065	16.7	3.2		48049			34.7

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)
	2.8	2.9	90		0.217	4.4		4322

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	40	45582	2429	100	0.20656	0.2065	0.20361	0.26325	RANDOM	34.708

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]
0.24			1.09		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.303
r_symmetry_vdw_refined	0.259
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13017
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	160

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement