3BDF | pdb_00003bdf

Crystal structure of metal-free E. coli alkaline phosphatase (T155V)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ED9	PDB Entry 1ED9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES, 0.2 M LiSO4, 1 mM ZnCl2, 5 mM MgCl2, 25-30% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.503	α = 90
b = 103.634	β = 105.8
c = 88.55	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 315	Vertical focusing mirror, single crystal (Si111) bent monochromator (horizontal focusing)	2007-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.00	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	50		0.051	21.7	3.2		210186

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)
	1.4	1.45			0.333	2.1	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB Entry 1ED9	1.4	50	183759	9184	97.26	0.163	0.162	0.16	0.184	0.1831	RANDOM	15.036

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]
0.16		-0.39	-0.18		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.447
r_dihedral_angle_4_deg	16.89
r_dihedral_angle_3_deg	12.242
r_dihedral_angle_1_deg	6.102
r_scangle_it	3.669
r_scbond_it	2.355
r_mcangle_it	1.518
r_angle_refined_deg	1.51
r_mcbond_it	0.936
r_nbtor_refined	0.301
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.196
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6577
Nucleic Acid Atoms
Solvent Atoms	1222
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing