3B35 | pdb_00003b35

Crystal structure of the M180A 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
2.49	50.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.148	α = 90
b = 109.148	β = 90
c = 90.99	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)	R Merge 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	1.1	41		0.059				122065			14.6

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				2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1AMP	1.1	41	122065	6145	95.04	0.15	0.149	0.15	0.166	0.17	RANDOM	14.646

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	37.163
r_dihedral_angle_4_deg	18.861
r_dihedral_angle_3_deg	11.358
r_sphericity_free	8.116
r_dihedral_angle_1_deg	6.317
r_sphericity_bonded	4.131
r_scangle_it	3.425
r_scbond_it	2.516
r_mcangle_it	1.892
r_angle_refined_deg	1.533
r_rigid_bond_restr	1.44
r_mcbond_it	1.313
r_symmetry_vdw_refined	0.31
r_nbtor_refined	0.306
r_nbd_refined	0.285
r_symmetry_hbond_refined	0.256
r_xyhbond_nbd_refined	0.227
r_chiral_restr	0.101
r_metal_ion_refined	0.077
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2522
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	15

Software

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