4RE5 | pdb_00004re5

Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HU5	PDB entry 2HU5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	78 mM sodium acetate buffer, 2.4% w/v PEG Mw4000, 6.7mM dithiothreitol and 0.44 mM EDTA. The protein was co-crystallized with the inhibitor., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.813	α = 90
b = 104.43	β = 90
c = 170.08	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 IV++	mirrors (Blue)	2010-11-15	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	1.9	20	99.7	0.062	17.58	3.93	90022	90022		-3	32.79

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	1.9	1.95	99.9		0.682	2.27	3.81

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 (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 2HU5	1.9	19.93	85520	85520	4499	99.66	0.17902	0.17902	0.17695	0.18	0.2181	0.23	RANDOM, imported from isostructural data set of pdb entry 2HU5	35.253

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]
-0.31			-1.37		1.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.581
r_dihedral_angle_4_deg	18.933
r_dihedral_angle_3_deg	13.426
r_long_range_B_refined	7.089
r_long_range_B_other	7.089
r_dihedral_angle_1_deg	6.303
r_scangle_other	3.994
r_mcangle_it	2.735
r_mcangle_other	2.735
r_scbond_it	2.68
r_scbond_other	2.679
r_mcbond_it	1.876
r_mcbond_other	1.876
r_angle_refined_deg	1.72
r_angle_other_deg	1.14
r_chiral_restr	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.006
r_gen_planes_other	0.005
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	8591
Nucleic Acid Atoms
Solvent Atoms	662
Heterogen Atoms	69

Software

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