2ANU | pdb_00002anu

Crystal structure of Predicted metal-dependent phosphoesterase (PHP family) (tm0559) from THERMOTOGA MARITIMA at 2.40 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	277	0.1M KH2PO4, 2.0M NaCl, 0.1M NaH2PO4, 0.1M MES , pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.307	α = 90
b = 111.307	β = 90
c = 383.222	γ = 120

Symmetry
Space Group	H 3

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	flat mirror	2005-04-08	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2005-03-31	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.953690	SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.89194, 0.97944	SSRL	BL9-2

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	2.26	29.1	99.5	0.13	0.13	4.5	3.4		83429

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	2.26	2.32		99.4	0.707	0.707	1	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.4	29	65772	3516	99.99	0.172	0.169	0.18	0.22	0.2	RANDOM	30.366

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]
-1.23	-0.61		-1.23		1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.934
r_dihedral_angle_4_deg	18.129
r_dihedral_angle_3_deg	16.499
r_dihedral_angle_1_deg	7.168
r_scangle_it	5.222
r_scbond_it	3.947
r_mcangle_it	2.18
r_mcbond_it	1.863
r_angle_refined_deg	1.349
r_angle_other_deg	0.771
r_mcbond_other	0.557
r_symmetry_vdw_other	0.22
r_nbd_refined	0.201
r_nbtor_refined	0.18
r_nbd_other	0.175
r_symmetry_hbond_refined	0.142
r_xyhbond_nbd_refined	0.139
r_symmetry_vdw_refined	0.129
r_nbtor_other	0.086
r_chiral_restr	0.076
r_metal_ion_refined	0.046
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10920
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SHELXE	model building