2O2X | pdb_00002o2x

Crystal structure of a putative had-like phosphatase (mll2559) from mesorhizobium loti at 1.50 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	6.64	277	28.5% polyethylene glycol 6000, 0.1M HEPES pH 6.64, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.48	α = 90
b = 66.27	β = 108.53
c = 41.02	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2006-11-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97978	SSRL	BL11-1

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	1.5	28.262	94.8	0.046	11.11	3.71		29534			12.94

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	1.5	1.55	88.8		0.271	2.88		4527

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.5	28.262	29513	1499	99.57	0.139	0.138	0.15	0.167	0.18	RANDOM	13.085

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]
0.26		-0.75	-0.22		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.741
r_dihedral_angle_4_deg	16.713
r_dihedral_angle_3_deg	10.84
r_dihedral_angle_1_deg	5.645
r_scangle_it	5.59
r_scbond_it	3.621
r_mcangle_it	2.337
r_mcbond_it	1.72
r_angle_refined_deg	1.457
r_angle_other_deg	0.826
r_mcbond_other	0.405
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.189
r_nbd_other	0.187
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.175
r_symmetry_vdw_other	0.17
r_symmetry_vdw_refined	0.105
r_chiral_restr	0.084
r_nbtor_other	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1566
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	12

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing