3GI7 | pdb_00003gi7

Crystal structure of a duf1311 family protein (pp0307) from pseudomonas putida kt2440 at 1.85 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.67	293	NANODROP, 2.10M Ammonium sulfate, 0.250M Potassium sodium tartrate, 0.1M Sodium citrate - citric acid pH 5.67, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.027	α = 90
b = 100.027	β = 90
c = 58.343	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	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-01-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162, 0.97964, 0.97949	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.85	29.173	100	0.065	0.065	0.07	18.5	7.2		25875			31.628

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	1.85	1.9	100		0.692	0.692	2.7	7.3	1880

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	1.85	29.173	25827	1314	99.96	0.179	0.178	0.19	0.199	0.22	RANDOM	25.285

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]
0.17			0.17		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.536
r_dihedral_angle_4_deg	19.668
r_dihedral_angle_3_deg	12.441
r_scangle_it	7.981
r_scbond_it	5.423
r_dihedral_angle_1_deg	4.235
r_mcangle_it	2.862
r_mcbond_it	1.798
r_angle_refined_deg	1.486
r_angle_other_deg	1.178

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.536
r_dihedral_angle_4_deg	19.668
r_dihedral_angle_3_deg	12.441
r_scangle_it	7.981
r_scbond_it	5.423
r_dihedral_angle_1_deg	4.235
r_mcangle_it	2.862
r_mcbond_it	1.798
r_angle_refined_deg	1.486
r_angle_other_deg	1.178
r_mcbond_other	0.717
r_chiral_restr	0.151
r_bond_refined_d	0.018
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1561
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.