2B8J | pdb_00002b8j

Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with adenosine and phosphate at 2 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N8N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	298	AphA 6mg/mL, 50 mM Na acetate, 25% PEG 6000, 10mM AMP, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.966	α = 90
b = 66.544	β = 124.02
c = 91.544	γ = 90

Symmetry
Space Group	C 1 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	MARRESEARCH	Double-crystal monochromator	2003-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	1.001	ELETTRA	5.2R

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.033	49.65	97.4	0.077	0.077	6.2	3	28127	28127			19.44

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.033	2.14	89.6		0.147	0.147	4.2	2.5	3767

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	MOLECULAR REPLACEMENT	THROUGHOUT	1N8N	2.033	49.39	25795	25795	2330	100	0.17545	0.17545	0.17123	0.18	0.22258	0.23	RANDOM	18.581

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]
-0.43		-0.84	-0.75		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.108
r_dihedral_angle_4_deg	16.857
r_dihedral_angle_3_deg	14.273
r_dihedral_angle_1_deg	6.162
r_scangle_it	4.117
r_scbond_it	2.578
r_angle_refined_deg	1.591
r_mcangle_it	1.56
r_mcbond_it	0.869
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.222
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.108
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_metal_ion_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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	3314
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	42

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling