3DDD | pdb_00003ddd

Crystal structure of A Putative Acetyltransferase (NP_142035.1) from PYROCOCCUS HORIKOSHII at 2.25 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.8M sodium citrate, 0.3M sodium chloride, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.673	α = 90
b = 113.673	β = 90
c = 70.756	γ = 90

Symmetry
Space Group	P 43 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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.25	29.037	100	0.129	0.129	4.9	7.2		22597			38.144

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	2.25	2.31	100		0.815	0.815	0.9	7.3	1648

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	2.25	29.037	22552	1154	99.92	0.171	0.168	0.17	0.221	0.22	RANDOM	31.366

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]
-1.8			-1.8		3.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.615
r_dihedral_angle_4_deg	19.683
r_dihedral_angle_3_deg	15.522
r_scangle_it	6.637
r_dihedral_angle_1_deg	6.586
r_scbond_it	5.384
r_mcangle_it	2.894
r_mcbond_it	2.035
r_angle_refined_deg	1.635
r_angle_other_deg	0.957
r_mcbond_other	0.473
r_symmetry_vdw_other	0.317
r_nbd_other	0.203
r_nbd_refined	0.199
r_nbtor_refined	0.182
r_symmetry_vdw_refined	0.16
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.139
r_nbtor_other	0.089
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2253
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
autoSHARP	phasing
SHELXD	phasing