3B3V

Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.317	α = 90
b = 109.317	β = 90
c = 91.003	γ = 120

Symmetry
Space Group	P 61 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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90010	APS	14-BM-C

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	1.22	21.72				92234	92234

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1AMP	1.22	21.72	92234	4637	97.3	0.15	0.149	0.171	RANDOM	15.041

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]
-0.1	-0.05		-0.1		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.866
r_dihedral_angle_4_deg	19.001
r_sphericity_free	13.922
r_dihedral_angle_3_deg	11.825
r_sphericity_bonded	7.834
r_dihedral_angle_1_deg	6.371
r_scangle_it	4.996
r_scbond_it	3.599
r_mcangle_it	2.58
r_mcbond_it	1.819
r_rigid_bond_restr	1.746
r_angle_refined_deg	1.67
r_mcbond_other	1.24
r_angle_other_deg	1.019
r_symmetry_vdw_other	0.324
r_symmetry_vdw_refined	0.297
r_nbd_refined	0.259
r_xyhbond_nbd_refined	0.228
r_symmetry_hbond_refined	0.227
r_nbd_other	0.209
r_nbtor_refined	0.181
r_chiral_restr	0.105
r_nbtor_other	0.089
r_metal_ion_refined	0.034
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2382
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	19

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing