2HU5

Binding of inhibitors by Acylaminoacyl-peptidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VE6	PDB ENTRY 1VE6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	78mM sodium acetate, 0.44mM EDTA, 2.2%PEG 4000, 0.56% beta-octyl-glucoside, 10% DMSO, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.4	α = 90
b = 103.334	β = 90
c = 168.224	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	IMAGE PLATE	RIGAKU RAXIS IIC		2005-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	19.726	89.1	0.098	15.12			67288		-3

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	2.1	53.3		0.56	2.7		5399

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1VE6	2	19.726	63906	63906	3377	89.26	0.18363	0.18363	0.18147	0.22441	RANDOM	17.716

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			-0.04		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.469
r_scangle_it	2.617
r_scbond_it	1.551
r_angle_refined_deg	1.308
r_mcangle_it	0.88
r_angle_other_deg	0.762
r_mcbond_it	0.472
r_symmetry_vdw_other	0.259
r_nbd_other	0.248
r_symmetry_vdw_refined	0.231
r_symmetry_hbond_refined	0.2
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.145
r_nbtor_other	0.088
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8658
Nucleic Acid Atoms
Solvent Atoms	332
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing