3MHB | pdb_00003mhb

Crystal structure of Staphylococcal nuclease variant Delta+PHS L38A at cryogenic temperature

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 all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, L36A, L37A, L38A, K64A, D77A T82A, Y91A, Y113A, V114A, Y115A and N118A; all b-factors were reset to 20.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	277	25% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.04	α = 90
b = 60.576	β = 93.29
c = 38.165	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	ADSC QUANTUM 315		2010-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1000	NSLS	X25

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	1.55	60	99.2	0.052	17.2	6.9	20512	20512			30.7

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	1.55	1.58	92.9		0.282		5.8	923

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	3BDC with all H2Os, Ca2+ and THP removed and the following truncations: H8A, T13A, Q30A, L36A, L37A, L38A, K64A, D77A T82A, Y91A, Y113A, V114A, Y115A and N118A; all b-factors were reset to 20.	1.55	30.99	20355	20355	2030	99.24	0.2001	0.193	0.188	0.1875	0.238	0.2347	RANDOM	22.598

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]
-1.09		0.59	-1		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.43
r_dihedral_angle_3_deg	16.852
r_dihedral_angle_4_deg	11.9
r_dihedral_angle_1_deg	6.054
r_scangle_it	4.935
r_scbond_it	3.297
r_angle_refined_deg	2.217
r_mcangle_it	2.195
r_mcbond_it	1.443
r_chiral_restr	0.145
r_bond_refined_d	0.024
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1030
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	26

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction