Experiment: 4KNL

Crystal structure of Staphylococcus aureus hydrolase AmiA in complex with its ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KNK	PDB ENTRY 4KNK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	0.1 M MES/imidazole, pH 6.5, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M sodium citrate, 0.02 M racemic sodium/potassium tartrate, 0.02 M sodium oxamate, 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% w/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.81	α = 90
b = 82.83	β = 96.18
c = 77.43	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	PIXEL	DECTRIS PILATUS 6M		2012-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.00605	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.55	48.21	99.1	13.9	3.6		122961	-3	-3	24.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59	98.1		1.7	3	8927

Refinement

Statistics
Diffraction ID	Structure Solution 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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 4KNK	1.55	48.209	1.99	124130	122657	6129	99.48	0.1725	0.1712	0.1981	0.1881	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.229
f_angle_d	1.382
f_chiral_restr	0.095
f_bond_d	0.012
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6628
Nucleic Acid Atoms
Solvent Atoms	630
Heterogen Atoms	58

Software

Software
Software Name	Purpose
RemDAq	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling