2HU7

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, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.682	α = 90
b = 103.989	β = 90
c = 168.594	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		2005-06-03	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	19.537	94.8	0.115	13.07			76464		-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	80.2		0.383	3.1		8216

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	2.01	19.52	68079	68079	3602	94.75	0.17761	0.17761	0.17554	0.21693	RANDOM (AS FOR RELATED PDB ENTRY 2HU5)	17.854

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]
-0.07			-0.06		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.421
r_scangle_it	1.968
r_mcangle_it	1.747
r_angle_refined_deg	1.274
r_scbond_it	1.21
r_mcbond_it	1.087
r_angle_other_deg	0.838
r_symmetry_vdw_refined	0.266
r_nbd_other	0.248
r_symmetry_vdw_other	0.248
r_nbd_refined	0.195
r_symmetry_hbond_refined	0.183
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.086
r_nbtor_other	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	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	8623
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	42

Software

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