3HK4 | pdb_00003hk4

CRYSTAL STRUCTURE OF A PUTATIVE SNOAL-LIKE POLYKETIDE CYCLASE [CARBOHYDRATE PHOSPHATASE] (MLR7391) FROM MESORHIZOBIUM LOTI AT 1.96 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.6	293	0.3000 M magnesium chloride, 24.0000% polyethylene glycol 8000, 0.1M TRIS pH 8.6, VAPOR DIFFUSION, SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.183	α = 88.77
b = 54.778	β = 84.91
c = 63.844	γ = 73.56

Symmetry
Space Group	P 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)	2009-02-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97894,0.97833	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	1.96	28.352	89.1	0.045	9.82	2.02		37927		-3	26.47

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	1.96	2.03	86		0.201	1.9

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	1.96	28.352	37925	1903	96.7	0.179	0.177	0.18	0.22	0.22	RANDOM	35.285

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]
1.45	0.8	1.1	-0.9	-0.1	-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.436
r_dihedral_angle_4_deg	15.841
r_dihedral_angle_3_deg	11.851
r_scangle_it	8.225
r_scbond_it	6.234
r_dihedral_angle_1_deg	3.734
r_mcangle_it	3.232
r_mcbond_it	2.469
r_angle_refined_deg	1.659
r_angle_other_deg	0.946
r_mcbond_other	0.571
r_xyhbond_nbd_refined	0.216
r_symmetry_vdw_other	0.204
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.196
r_nbtor_refined	0.188
r_nbd_other	0.177
r_xyhbond_nbd_other	0.138
r_symmetry_vdw_refined	0.113
r_nbtor_other	0.09
r_chiral_restr	0.081
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3651
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms

Software

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