2G1A | pdb_00002g1a

Crystal structure of the complex between Apha class B acid phosphatase/phosphotransferase

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	Drop: aphA 6mg/ml, MG2+ 10mM, PMEA 10mM. Reservoir solution: 50mM Na acetate, 0.6% (w/v) Spermine tetrahydrochloride, 22% PEG6000, pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.914	α = 90
b = 66.287	β = 121.06
c = 91.841	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	ADSC QUANTUM 4		2005-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934000	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	2	50.7	96.4	0.055	0.055				30906

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	2.11	79.6		0.036

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	PDB code 1N8N	2	50.7	28110	28110	2791	100	0.16339	0.16339	0.15956	0.16	0.20115	0.2	RANDOM	10.313

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]
0.07		0.36	-0.28		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.436
r_dihedral_angle_4_deg	21.497
r_dihedral_angle_3_deg	14.055
r_sphericity_free	7.253
r_dihedral_angle_1_deg	5.849
r_scangle_it	3.259
r_scbond_it	2.101
r_angle_refined_deg	1.398
r_mcangle_it	1.126
r_mcbond_it	0.686

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.436
r_dihedral_angle_4_deg	21.497
r_dihedral_angle_3_deg	14.055
r_sphericity_free	7.253
r_dihedral_angle_1_deg	5.849
r_scangle_it	3.259
r_scbond_it	2.101
r_angle_refined_deg	1.398
r_mcangle_it	1.126
r_mcbond_it	0.686
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.214
r_nbd_refined	0.194
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3286
Nucleic Acid Atoms
Solvent Atoms	639
Heterogen Atoms	38

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.