3B3T

Crystal structure of the D118N 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	50.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.294	α = 90
b = 109.294	β = 90
c = 91.009	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	100					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	1.17	42				102258	102258

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	1.17	42	102258	5101	95.35	0.143	0.142	0.161	RANDOM	11.391

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]
0.01	0.01		0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.091
r_dihedral_angle_4_deg	22.371
r_dihedral_angle_3_deg	11.263
r_sphericity_free	9.694
r_dihedral_angle_1_deg	6.114
r_sphericity_bonded	5.079
r_scangle_it	4.328
r_scbond_it	3.047
r_mcangle_it	2.209
r_symmetry_metal_ion_refined	1.62
r_angle_refined_deg	1.617
r_mcbond_it	1.532
r_rigid_bond_restr	1.525
r_angle_other_deg	0.968
r_mcbond_other	0.851
r_symmetry_vdw_refined	0.423
r_symmetry_vdw_other	0.371
r_nbd_refined	0.242
r_nbd_other	0.201
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.179
r_chiral_restr	0.097
r_nbtor_other	0.09
r_metal_ion_refined	0.05
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2321
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	20

Software

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