3MYX | pdb_00003myx

Crystal structure of a PSPTO_0244 (Protein with unknown function which belongs to Pfam DUF861 family) from Pseudomonas syringae pv. tomato str. DC3000 at 1.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	277	0.2000M NH4Cl, 20.0000% PEG-3350, No Buffer pH 6.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.584	α = 90
b = 48.396	β = 108.21
c = 80.454	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-12-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97913,0.97879	SSRL	BL11-1

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	1.3	28.759	96.4	0.042	12.07			101752		-3	8.663

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)
	1.3	1.35	80.3		0.308	2.4

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	MAD	THROUGHOUT	1.3	28.759	101735	5084	98.27	0.119	0.117	0.12	0.146	0.15	RANDOM	13.022

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]
-0.11		-0.06	0.34		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.822
r_dihedral_angle_4_deg	17.832
r_dihedral_angle_3_deg	11.871
r_dihedral_angle_1_deg	7.071
r_sphericity_free	5.668
r_scangle_it	4.03
r_scbond_it	2.916
r_sphericity_bonded	2.739
r_mcangle_it	2.467
r_mcbond_it	1.68
r_angle_refined_deg	1.495
r_rigid_bond_restr	1.224
r_mcbond_other	0.971
r_angle_other_deg	0.85
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3504
Nucleic Acid Atoms
Solvent Atoms	791
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction