1MV8 | pdb_00001mv8

1.55 A crystal structure of a ternary complex of GDP-mannose dehydrogenase from Psuedomonas aeruginosa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MUU	PDB entry 1MUU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6		8%v/v methyl propane diol, 0.1M Na Acetate, 1mM DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.472	α = 90
b = 82.472	β = 90
c = 309.893	γ = 90

Symmetry
Space Group	P 43

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	SBC-2	Rosenbaum-Rock monochromator	2001-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-ID

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	1.55	40	99	0.123	9.1	5.4		294277

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	1.55	1.61	97		0.391	2.1		28757

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 (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1MUU	1.55	40	269565	14342	100	0.17535	0.1753	0.17434	0.15	0.19441	0.16	RANDOM	9.287

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]
0.12			0.12		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.173
r_dihedral_angle_1_deg	3.816
r_scangle_it	2.523
r_scbond_it	1.571
r_angle_refined_deg	1.389
r_mcangle_it	0.834
r_angle_other_deg	0.742
r_xyhbond_nbd_other	0.477
r_mcbond_it	0.45
r_symmetry_vdw_refined	0.336
r_symmetry_vdw_other	0.238
r_symmetry_hbond_refined	0.229
r_nbd_refined	0.225
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13141
Nucleic Acid Atoms
Solvent Atoms	1376
Heterogen Atoms	362

Software

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