3FGV | pdb_00003fgv

CRYSTAL STRUCTURE OF A PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE (SPO2313) FROM SILICIBACTER POMEROYI DSS-3 AT 1.30 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	0.2000M NH4I, 20.0000% PEG-3350, No Buffer pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.76	α = 90
b = 78.76	β = 90
c = 69.81	γ = 120

Symmetry
Space Group	P 65

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	0.94645,0.97967	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	1.3	26.118	98.7	0.06	14.22			60325		-3	10.966

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)
	1.3	1.35	96.6		0.435	2.6

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	1.3	26.118	60282	3041	99.87	0.131	0.13	0.14	0.15	0.16	RANDOM	14.97

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]
0.02	0.01		0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
TORSION ANGLES, PERUNL 2 (DEGREES)	34.886
TORSION ANGLES, PERUNL 4 (DEGREES)	17.18
TORSION ANGLES, PERUNL 3 (DEGREES)	13.462
r_sphericity_free	6.198
TORSION ANGLES, PERUNL 1 (DEGREES)	5.285
r_scangle_it	4.724
r_scbond_it	3.551
r_sphericity_bonded	3.087
r_mcangle_it	2.376
r_angle_other_deg	1.69
r_angle_refined_deg	1.665
r_mcbond_it	1.611
r_rigid_bond_restr	1.316
r_mcbond_other	0.793
r_symmetry_vdw_other	0.253
r_nbd_refined	0.195
r_nbtor_refined	0.171
r_nbd_other	0.165
r_symmetry_vdw_refined	0.149
r_chiral_restr	0.109
r_symmetry_hbond_refined	0.095
r_xyhbond_nbd_refined	0.089
r_nbtor_other	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1536
Nucleic Acid Atoms
Solvent Atoms	289
Heterogen Atoms	31

Software

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