4RE6 | pdb_00004re6

Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O4H	PDB ENTRY 3O4H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	78 mM sodium acetate buffer, 2.2% w/v PEG Mw4000, 5.2 mM dithiothreitol, 0.34 mM EDTA. Protein crystals were soaked in the inhibitor solution., pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.58	α = 105.15
b = 97.3	β = 103.96
c = 99.16	γ = 100.26

Symmetry
Space Group	P 1

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 210	Sagitally focusing Ge(220) and a multilayer	2011-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9334	ESRF	ID14-1

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	2.55	20	86.4	0.071	13.38	2.18	68281	68281		-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	2.55	2.62	51.1		0.505	2.16

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 3O4H	2.55	19.85	64833	64833	3441	86.52	0.21398	0.21152	0.21	0.25963	0.26	RANDOM, IMPORTED FROM ISOSTRUCTURAL DATA SET OF PDB ENTRY 3O4H.	33.726

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]
-0.14	0.42	0.11	0.63	0.14	-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.251
r_dihedral_angle_4_deg	17.548
r_dihedral_angle_3_deg	15.06
r_dihedral_angle_1_deg	5.844
r_long_range_B_refined	5.192
r_long_range_B_other	5.151
r_scangle_other	3.458
r_mcangle_it	3.012
r_mcangle_other	2.969
r_scbond_it	2.226
r_scbond_other	2.184
r_mcbond_it	1.881
r_mcbond_other	1.881
r_angle_refined_deg	1.47
r_angle_other_deg	1.294
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.006
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17267
Nucleic Acid Atoms
Solvent Atoms	674
Heterogen Atoms	49

Software

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