4Q7F | pdb_00004q7f

1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with Adenosine.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QFK	pdb entry 3QFK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	295	Protein: 7.0 mg/mL, 0.5M Sodium chloride, Tris-HCl pH 7.2, 0.5 mM TCEP, 1 mM Adenosine; Screen: PEGs II (D1), 0.1M Sodium acetate, 0.1M Sodium HEPES, 22% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.584	α = 90
b = 86.452	β = 116.86
c = 95.647	γ = 90

Symmetry
Space Group	C 1 2 1

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 225 mm CCD	beryllium lenses	2014-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	1.98	30	98	0.102	0.102	16.7	5.1	44896	44896		-3	19

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	1.98	2.01	97.2		0.62	0.62	2.9	5.2	2238

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	pdb entry 3QFK	1.98	29.36	42209	42209	2236	97.96	0.18846	0.1869	0.2	0.21788	0.23	RANDOM	31.592

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]
0.29		0.88	5.7		-4.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.566
r_dihedral_angle_4_deg	11.416
r_dihedral_angle_3_deg	9.598
r_long_range_B_refined	6.308
r_long_range_B_other	6.143
r_dihedral_angle_1_deg	3.116
r_scangle_other	2.218
r_mcangle_it	1.875
r_mcangle_other	1.875
r_angle_refined_deg	1.493
r_scbond_it	1.423
r_scbond_other	1.422
r_mcbond_it	1.154
r_mcbond_other	1.154
r_angle_other_deg	0.746
r_chiral_restr	0.088
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4092
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms	20

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling