3ES1 | pdb_00003es1

Crystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	277	0.2M NaThioCyanate, 20.0% PEG-3350, No Buffer pH 6.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.33	α = 90
b = 78.33	β = 90
c = 107.32	γ = 120

Symmetry
Space Group	P 64 2 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	2008-08-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.92522,0.97932,0.97879	SSRL	BL9-2

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	1.91	28.665	98	0.147	13.43			15326		-3	22.05

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	1.91	1.98	97.4		0.011	2.1

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	1.91	28.665	15326	765	97.54	0.172	0.17	0.17	0.205	0.21	RANDOM	22.97

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]
0.96	0.48		0.96		-1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.891
r_dihedral_angle_4_deg	18.022
r_dihedral_angle_3_deg	13.223
r_dihedral_angle_1_deg	6.995
r_scangle_it	3.084
r_scbond_it	2.097
r_angle_refined_deg	1.571
r_angle_other_deg	1.413
r_mcangle_it	1.323
r_mcbond_it	0.815

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.891
r_dihedral_angle_4_deg	18.022
r_dihedral_angle_3_deg	13.223
r_dihedral_angle_1_deg	6.995
r_scangle_it	3.084
r_scbond_it	2.097
r_angle_refined_deg	1.571
r_angle_other_deg	1.413
r_mcangle_it	1.323
r_mcbond_it	0.815
r_mcbond_other	0.226
r_chiral_restr	0.089
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1237
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	1

Software

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