Experiment: 1N8N

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	0.1795	0.20698	0.2085	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