2RB5

X-ray Crystallographic Structures Show Conservation of a Trigonal-Bipyramidal Intermediate in a Phosphoryl-transfer Superfamily.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	15%PEG 1500, 10mM magnesium chloride and 5mM sodium tungstate., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.95	46.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.387	α = 90
b = 56.467	β = 90
c = 94.447	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 210	mirrors	2006-06-21	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)	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	1.03	50	95.5	0.075	0.075	32	13.3	124944	124944	2	2	6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.03	1.07	75.3		0.479	0.036	3.6	5.8	9738

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO	FREE R	1YMQ	1.03	10	2	124767	124767	12486	95.5	0.1118	0.1104	0.1104	0.1363	RANDOM	15.2

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]
1.84			-0.95		-0.89

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
16	1903	2532

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.112
s_non_zero_chiral_vol	0.091
s_zero_chiral_vol	0.084
s_similar_adp_cmpnt	0.035
s_angle_d	0.034
s_from_restr_planes	0.029
s_anti_bump_dis_restr	0.022
s_bond_d	0.016
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2025
Nucleic Acid Atoms
Solvent Atoms	501
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHELX	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.