3KZW | pdb_00003kzw

Crystal structure of cytosol aminopeptidase from Staphylococcus aureus COL

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	70% MPD, 0.1M HEPES, pH 7.5, 0.5M sodium chloride, 0.01M Tris-HCl, pH 8.3, JCSG+, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.383	α = 90
b = 154.733	β = 90
c = 340.101	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	MARMOSAIC 225 mm CCD	Beryllium lenses	2008-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.7	44.62	98.8	0.139	0.139	9.19	4.8	207017	204154

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1gyt	2.7	44.62	207017	155647	8205	79.15	0.22234	0.22234	0.22139	0.2402	0.229	RANDOM	4.572

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]
			0.87		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.524
r_dihedral_angle_4_deg	13.611
r_dihedral_angle_3_deg	13.258
r_dihedral_angle_1_deg	4.668
r_angle_refined_deg	0.841
r_scangle_it	0.31
r_mcangle_it	0.25
r_scbond_it	0.18
r_mcbond_it	0.138
r_chiral_restr	0.057
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	45906
Nucleic Acid Atoms
Solvent Atoms	698
Heterogen Atoms	106

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling