4DYO | pdb_00004dyo

Crystal Structure of Human Aspartyl Aminopeptidase (DNPEP) in complex with Aspartic acid Hydroxamate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IJZ	PDB ENTRY 2IJZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293.15	15% PEG3350, 0.25 M magnesium chloride, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 244.595	α = 90
b = 244.595	β = 90
c = 244.595	γ = 90

Symmetry
Space Group	F 4 3 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	CCD	ADSC QUANTUM 315	Kirkpatrick Baez bimorph mirror pair	2009-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.2	56.11	99.6	0.179	10.4	10.8	32192	32185			28.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	97.5		0.833	2.2	8	4486

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	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 2IJZ	2.2	54.69	2	32185	30955	1230	99.5	0.156	0.1547	0.1558	0.1947	0.1985	RANDOM	25.863

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
r_sphericity_free	40.498
r_dihedral_angle_2_deg	38.45
r_dihedral_angle_4_deg	16.824
r_dihedral_angle_3_deg	13.794
r_scangle_it	9.385
r_scbond_it	7.211
r_dihedral_angle_1_deg	6.516
r_mcangle_it	4.217
r_sphericity_bonded	3.031
r_mcbond_it	2.781
r_angle_refined_deg	1.522
r_angle_other_deg	0.932
r_mcbond_other	0.867
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3531
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	49

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling