1RMT | pdb_00001rmt

Crystal structure of AphA class B acid phosphatase/phosphotransferase complexed with adenosine.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	Crystallization components* AphA 6mg/mL, 50mM Na acetate, 25% PEG 6000, 10mM adenosine, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.74	α = 90
b = 66.704	β = 117.13
c = 88.556	γ = 90

Symmetry
Space Group	P 1 21 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 4		2002-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.96111	ESRF	ID14-1

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	1.4	75.419		0.099	0.099	3.7	3.4	153897	153897

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	1.4	1.48	59.3		0.452	0.452	1.6	2.3

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1N8N	1.4	74.54	142874	142874	11010	100	0.16906	0.16669	0.18	0.19908	0.21	RANDOM	11.611

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]
0.29		0.08	-0.33		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.791
r_scangle_it	3.574
r_sphericity_free	3.3
r_sphericity_bonded	2.386
r_scbond_it	2.368
r_mcangle_it	1.68
r_angle_refined_deg	1.558
r_rigid_bond_restr	1.285
r_mcbond_it	1.14
r_angle_other_deg	0.853
r_symmetry_vdw_other	0.299
r_nbd_other	0.259
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.22
r_symmetry_hbond_refined	0.216
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.087
r_nbtor_other	0.083
r_metal_ion_refined	0.018
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.006
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_other
r_symmetry_hbond_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6590
Nucleic Acid Atoms
Solvent Atoms	1233
Heterogen Atoms	80

Software

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