3EHC | pdb_00003ehc

Crystal structure of a snoal-like polyketide cyclase (atu3018) from agrobacterium tumefaciens str. c58 at 2.12 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	1.5000M (NH4)2SO4, 12.0000% Glycerol, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.1	α = 90
b = 114.06	β = 90
c = 137.99	γ = 90

Symmetry
Space Group	P 21 21 21

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 collimating mirror, toroid focusing mirror	2008-08-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162, 0.97920, 0.97932	SSRL	BL9-2

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	2.12	29.514	98.3	0.065	8.77	3.63		47190		-3	34.929

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	2.12	2.2	98.3		0.522	1.47

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	2.12	29.514	47114	2392	99.1	0.207	0.205	0.21	0.243	0.24	RANDOM	38.911

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]
1.83			-1.93		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.615
r_dihedral_angle_3_deg	14.57
r_dihedral_angle_4_deg	13.704
r_dihedral_angle_1_deg	6.302
r_scangle_it	5.826
r_scbond_it	4.287
r_mcangle_it	2.379
r_mcbond_it	1.575
r_angle_refined_deg	1.431
r_angle_other_deg	1.009
r_mcbond_other	0.307
r_symmetry_vdw_other	0.291
r_symmetry_hbond_refined	0.202
r_nbd_other	0.195
r_nbd_refined	0.185
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.17
r_symmetry_vdw_refined	0.141
r_chiral_restr	0.089
r_nbtor_other	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4137
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	46

Software

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