1OI8 | pdb_00001oi8

5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (P90C, L424C)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HO5	PDB ENTRY 1HO5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		1.8 M LI2SO4, 100MM TRIS, 1MM MNCL, 10 MM BETAINE, 10% 2-METHYL-2,4-PENTANDIOLE, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.689	α = 90
b = 97.689	β = 90
c = 312.051	γ = 90

Symmetry
Space Group	P 41 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	IMAGE PLATE	MARRESEARCH	MIRRORS, TRIANGULAR MONOCHROMATOR	2002-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	2.1	30	95.1	0.069	17.2	3.2		89316

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	2.1	2.18	95.6		0.267	4.7	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1HO5	2.1	19.96	80645	4255	95.3	0.159	0.156	0.17	0.205	0.17	RANDOM	22.26

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]
0.03			0.03		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.581
r_scangle_it	4.709
r_scbond_it	2.933
r_mcangle_it	1.754
r_angle_refined_deg	1.743
r_mcbond_it	0.97
r_angle_other_deg	0.922
r_symmetry_vdw_other	0.291
r_nbd_other	0.252
r_symmetry_hbond_refined	0.239
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.201
r_symmetry_vdw_refined	0.181
r_chiral_restr	0.114
r_nbtor_other	0.089
r_bond_refined_d	0.022
r_gen_planes_other	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8194
Nucleic Acid Atoms
Solvent Atoms	916
Heterogen Atoms	22

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
BEAST	phasing
REFMAC	refinement