2OLT | pdb_00002olt

Crystal structure of a phou-like protein (so_3770) from shewanella oneidensis mr-1 at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	277	NANODROP, 1.5M Sodium acetate, 0.1M Sodium cacodylate pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 1.0M Sodium citrate, 0.1M Sodium cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.53	α = 90
b = 99.53	β = 90
c = 395.92	γ = 120

Symmetry
Space Group	H 3 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		2006-09-14	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	ADSC QUANTUM 315	Flat mirror (vertical focusing)	2006-05-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.00000	ALS	8.2.2
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.918370, 0.979318, 0.979035	SSRL	BL11-1

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	2	29.16	99.9	0.058	13.4	5.5		51605			36

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	2.05	100		0.623		5.5	3630

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 (All)	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	29.16	51591	2634	99.84	0.205	0.205	0.203	0.22	0.242	0.25	RANDOM	39.759

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]
2.45	1.22		2.45		-3.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.873
r_dihedral_angle_3_deg	12.753
r_dihedral_angle_4_deg	10.545
r_scangle_it	3.815
r_dihedral_angle_1_deg	2.981
r_scbond_it	2.459
r_angle_refined_deg	1.565
r_mcangle_it	1.353
r_angle_other_deg	1.006
r_mcbond_it	0.956
r_symmetry_vdw_other	0.309
r_symmetry_hbond_refined	0.291
r_nbd_refined	0.232
r_mcbond_other	0.212
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.186
r_symmetry_vdw_refined	0.181
r_nbd_other	0.162
r_chiral_restr	0.109
r_nbtor_other	0.093
r_xyhbond_nbd_other	0.021
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4898
Nucleic Acid Atoms
Solvent Atoms	381
Heterogen Atoms	27

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SHARP	phasing