2RIL | pdb_00002ril

Crystal structure of a putative monooxygenase (YP_001095275.1) from Shewanella loihica PV-4 at 1.26 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.931	α = 90
b = 63.155	β = 90
c = 27.283	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	ADSC QUANTUM 315		2007-10-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537, 0.9797, 0.9795	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.26	26.528	63.3	0.059	0.059	6.5	3.2		14880

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.26	1.29	3.1		1.314	1.314	0.7	1	52

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	1.26	26.528	14848	742	63.01	0.141	0.14	0.15	0.162	0.17	RANDOM	10.501

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]
-0.1			-0.65		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.926
r_dihedral_angle_4_deg	16.783
r_dihedral_angle_3_deg	13.404
r_sphericity_free	8.418
r_dihedral_angle_1_deg	5.392
r_scangle_it	4.38
r_scbond_it	3.386
r_sphericity_bonded	3.36
r_rigid_bond_restr	2.186
r_mcangle_it	2.18
r_mcbond_it	1.775
r_angle_refined_deg	1.599
r_angle_other_deg	0.962
r_mcbond_other	0.663
r_symmetry_vdw_other	0.33
r_symmetry_vdw_refined	0.298
r_nbd_refined	0.216
r_nbd_other	0.198
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.106
r_nbtor_other	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	748
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SHELXD	phasing
SHARP	phasing