3E8M | pdb_00003e8m

Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K1E	pdb entry 1K1E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	30% w/v polyethelene glycol (PEG) 4,000, 0.1 M Tris HCl pH 8.5, 0.2 M sodium acetate and 10 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.243	α = 90
b = 107.482	β = 90
c = 75.093	γ = 90

Symmetry
Space Group	P 21 21 2

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 210	mirrors	2006-06-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.9000	NSLS	X12C

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	1.1	50	97.4	0.047	43.5	11.2		258326	2	2	8.1

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	1.14	84.8		0.29	3.8	4.2	22333

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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		FREE R	pdb entry 1K1E	1.1	28.782	1.89	257889	257759	24703	94.97	0.128	0.127	0.12	0.141	0.14	RANDOM	17.685

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]
-2.077			-1.633		-0.953

RMS Deviations
Key	Refinement Restraint Deviation
f_zero_chiral_vol	0.073
f_angle_d	0.031
f_from_restr_planes	0.026
f_bond_d	0.015
f_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10811
Nucleic Acid Atoms
Solvent Atoms	1197
Heterogen Atoms	171

Software

Software
Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOLREP	phasing
DENZO	data reduction

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.