3N07 | pdb_00003n07

Structure of putative 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Vibrio cholerae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	0.1M Bis-Tris pH 6.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.946	α = 90
b = 77.109	β = 106.65
c = 78.5	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 QUANTUM 315		2010-03-28		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A

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	1.76	50	99	0.087	12.9	6.2		72199

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	1.76	1.79	81		0.6		5.4	2942

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	SAD	THROUGHOUT	1.76	50	72063	3634	99.17	0.172	0.17	0.18	0.201	0.21	RANDOM	29.816

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]
-0.94		-0.4	-0.61		1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.158
r_dihedral_angle_3_deg	13.807
r_dihedral_angle_4_deg	8.803
r_dihedral_angle_1_deg	5.441
r_scangle_it	3.795
r_scbond_it	2.293
r_mcangle_it	1.389
r_angle_refined_deg	1.341
r_mcbond_it	0.764
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.158
r_dihedral_angle_3_deg	13.807
r_dihedral_angle_4_deg	8.803
r_dihedral_angle_1_deg	5.441
r_scangle_it	3.795
r_scbond_it	2.293
r_mcangle_it	1.389
r_angle_refined_deg	1.341
r_mcbond_it	0.764
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5462
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL2Map	phasing
CCP4	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.