3QOL | pdb_00003qol

Crystal structure of Staphylococcal nuclease variant D+PHS/V23E at pH 6 determined at 100 K

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BDC	3BDC WITH NON-PROTEIN ATOMS REMOVED, B-FACTORS SET TO 20 AND RESIDUES 23,113-116 CHANGED TO ALA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	277	22% MPD, 25 mM Potassium Phosphate, pdTp, CaCl2, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.033	α = 90
b = 60.453	β = 94.44
c = 37.626	γ = 90

Symmetry
Space Group	P 1 21 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	APEX II CCD	MULTI-LAYER OPTICS	2009-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE

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	1.9	37.51	99.6	0.0365	41.19	12.13		11002			29.9

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	1.9	1.94	99.7		0.2139	5.68	5.21

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	3BDC WITH NON-PROTEIN ATOMS REMOVED, B-FACTORS SET TO 20 AND RESIDUES 23,113-116 CHANGED TO ALA	1.9	37.51	10474	10474	528	100	0.189	0.187	0.19	0.227	0.23	RANDOM	41.46

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]
-0.12		0.15	-0.02		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.259
r_dihedral_angle_3_deg	16.444
r_dihedral_angle_4_deg	6.915
r_dihedral_angle_1_deg	6.546
r_scangle_it	5.523
r_scbond_it	3.518
r_mcangle_it	2.522
r_angle_refined_deg	1.695
r_mcbond_it	1.467
r_chiral_restr	0.133
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1035
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	26

Software

Software
Software Name	Purpose
APEX	data collection
PHASER	phasing
REFMAC	refinement
SAINT	data reduction
XPREP	data reduction