4WR2 | pdb_00004wr2

Crystal structure of a putative pyrimidine-specific ribonucleoside hydrolase (RihA) Protein from Shewanella loihica PV-4 (SHEW_0697, Target PSI-029635) with divalent cation and PEG 400 bound at the active site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	Protein (18.02 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) was combined with an equal volume of Reservoir (100 mM Sodium Citrate pH 5.5, 40% PEG 600), Cryoprotection (100 mM Sodium Citrate pH 5.5, 40% PEG 600)

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.078	α = 90
b = 115.047	β = 90
c = 141.64	γ = 90

Symmetry
Space Group	I 2 2 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	RAYONIX MX225HE	MIRRORS	2013-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97931	APS	31-ID

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	1.7	30	99.5	0.078	0.078	8.6	7.7		104560			22.82

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	1.7	1.76	99.2		0.97		7.6	10451

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	SAD	THROUGHOUT	1.7	29.767	104560	1997	99.19	0.1572	0.1566	0.1543	0.1713	0.1693	RANDOM	31.367

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]
3.2			-1.64		-1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.8
r_dihedral_angle_4_deg	23.519
r_sphericity_bonded	12.078
r_dihedral_angle_3_deg	10.772
r_dihedral_angle_1_deg	7.324
r_rigid_bond_restr	6.133
r_angle_other_deg	1.839
r_angle_refined_deg	1.312
r_mcangle_it	1.189
r_mcbond_it	1.132
r_mcbond_other	1.123
r_chiral_restr	0.065
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2345
Nucleic Acid Atoms
Solvent Atoms	284
Heterogen Atoms	33

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHENIX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction