3F7S | pdb_00003f7s

CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (PP_4556) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.11 A RESOLUTION

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	10.5	277	0.8000M K2HPO4, 0.2000M Li2SO4, 1.2000M NaH2PO4, 0.1M CAPS pH 10.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.92	α = 90
b = 65.92	β = 90
c = 89.39	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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B		APS	23-ID-B

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	2.11	29.476	99.9	0.12	9.68			11917		-3	31.836

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	2.11	2.19	99.9		0.986	1.6

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	2.11	29.476	11874	564	99.91	0.179	0.177	0.18	0.217	0.22	RANDOM	33.633

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]
-0.05			-0.05		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.877
r_dihedral_angle_3_deg	16.121
r_scangle_it	8.957
r_scbond_it	6.37
r_dihedral_angle_1_deg	6.192
r_dihedral_angle_4_deg	4.955
r_mcangle_it	3.785
r_mcbond_it	2.121
r_angle_refined_deg	1.517
r_angle_other_deg	0.928

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.877
r_dihedral_angle_3_deg	16.121
r_scangle_it	8.957
r_scbond_it	6.37
r_dihedral_angle_1_deg	6.192
r_dihedral_angle_4_deg	4.955
r_mcangle_it	3.785
r_mcbond_it	2.121
r_angle_refined_deg	1.517
r_angle_other_deg	0.928
r_mcbond_other	0.498
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1091
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	15

Software

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