3F8H | pdb_00003f8h

Crystal structure of a putative polyketide cyclase (tm1040_3560) from silicibacter sp. tm1040 at 2.00 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	0.0200M CaCl2, 30.0000% MPD, 0.1M Acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.31	α = 90
b = 63.31	β = 90
c = 196.09	γ = 90

Symmetry
Space Group	P 43 21 2

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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-10-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97967,0.94645	APS	23-ID-B

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	29.501	99.4	0.169	7.58			28101		-3	23.871

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	2.07	95.9		0.01	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	2	29.501	28016	1408	99.77	0.169	0.167	0.18	0.213	0.22	RANDOM	44.739

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]
0.73			0.73		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.722
r_dihedral_angle_4_deg	17.279
r_dihedral_angle_3_deg	10.753
r_scangle_it	6.105
r_scbond_it	4.331
r_dihedral_angle_1_deg	3.965
r_mcangle_it	2.462
r_angle_refined_deg	1.679
r_angle_other_deg	1.582
r_mcbond_it	1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.722
r_dihedral_angle_4_deg	17.279
r_dihedral_angle_3_deg	10.753
r_scangle_it	6.105
r_scbond_it	4.331
r_dihedral_angle_1_deg	3.965
r_mcangle_it	2.462
r_angle_refined_deg	1.679
r_angle_other_deg	1.582
r_mcbond_it	1.35
r_mcbond_other	0.288
r_chiral_restr	0.092
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2136
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	65

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.