2GLQ | pdb_00002glq

X-ray structure of human alkaline phosphatase in complex with strontium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Crystals were grown at 19 (2) using sitting drop vapor diffusion, with protein concentration of 10mg/ml, in the presence of 10mM p-nitrophenyl phosphate. Crystals were obtained from 12% PEG 3350, 100mM sodium cacodylate pH 6.5, 1mM zinc chloride, 2mM magnesium acetate, and 2mM strontium chloride over a period of five months, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.09	α = 90
b = 115.299	β = 90
c = 107.32	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200					M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	100	99	0.096	19.25		72276	72276

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.65	96.9		0.431	2.88

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.6	9.99	71854	68217	3637	99	0.14991	0.14991	0.14778	0.1602	0.18813	0.1948	RANDOM	17.399

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]
-0.03			0.1		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.904
r_scangle_it	4.373
r_sphericity_free	3.354
r_scbond_it	2.869
r_sphericity_bonded	2.116
r_mcangle_it	1.884
r_angle_refined_deg	1.751
r_rigid_bond_restr	1.599
r_mcbond_it	1.184
r_angle_other_deg	1.02
r_symmetry_vdw_other	0.301
r_nbd_refined	0.263
r_nbd_other	0.258
r_symmetry_hbond_refined	0.251
r_xyhbond_nbd_refined	0.215
r_symmetry_vdw_refined	0.161
r_chiral_restr	0.145
r_metal_ion_refined	0.127
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_other	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3660
Nucleic Acid Atoms
Solvent Atoms	597
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling