1V3Z | pdb_00001v3z

Crystal Structure of Acylphosphatase from Pyrococcus horikoshii

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.065	α = 90
b = 86.065	β = 90
c = 75.355	γ = 120

Symmetry
Space Group	P 32 2 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				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.9	SPring-8	BL41XU

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.72	30	32927	1721	100	0.16923	0.16819	0.18	0.19003	0.19	RANDOM	18.387

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]
0.65	0.33		0.65		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.921
r_scangle_it	5.647
r_scbond_it	3.268
r_mcangle_it	1.85
r_angle_refined_deg	1.484
r_mcbond_it	0.966
r_angle_other_deg	0.842
r_symmetry_vdw_other	0.328
r_nbd_other	0.265
r_nbd_refined	0.243
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.14
r_metal_ion_refined	0.115
r_chiral_restr	0.095
r_nbtor_other	0.077
r_bond_refined_d	0.016
r_gen_planes_other	0.014
r_gen_planes_refined	0.011
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_other
r_symmetry_vdw_refined
r_symmetry_hbond_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	1432
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling