1N8N | pdb_00001n8n

Crystal structure of the Au3+ complex of AphA class B acid phosphatase/phosphotransferase from E. coli at 1.69 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		MAD-phased Bromine derivative at 2.2 A resolution

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K. The crystals of the native enzyme (containing Mg2+ or Zn2+) have been soaked in 1 mM solution of AuCl3

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.279	α = 90
b = 92.457	β = 90
c = 138.182	γ = 90

Symmetry
Space Group	I 2 2 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 4	Toroidal mirror	2002-07-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.0377, 1.0404, 0.9392	ESRF	ID14-4

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	1.69	46.13	88.8	0.061	0.061	7	3.7	31884	31884			19.709

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	1.69	1.79	53		0.093	0.093	7	1.6	2976

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	MAD-phased Bromine derivative at 2.2 A resolution	1.69	46.13	31884	31884	1673	88.8	0.17906	0.17906	0.17759	0.18	0.20698	0.21	RANDOM	20.602

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]
1.63			-0.72		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.605
r_scangle_it	4.623
r_scbond_it	2.695
r_mcangle_it	1.634
r_angle_refined_deg	1.412
r_mcbond_it	0.898
r_symmetry_vdw_refined	0.234
r_symmetry_hbond_refined	0.223
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.605
r_scangle_it	4.623
r_scbond_it	2.695
r_mcangle_it	1.634
r_angle_refined_deg	1.412
r_mcbond_it	0.898
r_symmetry_vdw_refined	0.234
r_symmetry_hbond_refined	0.223
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1643
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

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.