2HFJ | pdb_00002hfj

Pikromycin thioesterase with covalent pentaketide affinity label

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	296	1.4M Li2SO4, 100mM HEPES pH 7.6, 80mM MgCl2, 2mM DTT, 5% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.686	α = 90
b = 131.063	β = 90
c = 56.864	γ = 90

Symmetry
Space Group	P 21 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		2006-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97922	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	50	99.6	0.073	22.7	6.9	59548	59323

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2.02	98.7		0.559	3.2	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	50	59548	56330	2932	99.57	0.20179	0.19973	0.1919	0.24018	0.2311	RANDOM	38.858

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]
-2.06			-0.95		3.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.498
r_dihedral_angle_4_deg	16.091
r_dihedral_angle_3_deg	14.936
r_dihedral_angle_1_deg	5.373
r_scangle_it	3.54
r_mcangle_it	3.508
r_mcbond_it	2.368
r_scbond_it	2.338
r_angle_refined_deg	1.286
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.206
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4257
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	41

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing