3NPP | pdb_00003npp

Crystal structure of a Pfam DUF1093 family protein (BSU39620) from Bacillus subtilis at 2.15 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	3.200000000M (NH4)2SO4, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.535	α = 90
b = 91.535	β = 90
c = 59.13	γ = 120

Symmetry
Space Group	P 3 2 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)	2010-04-08	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 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	2.15	29.962	100	0.112		6.1		15880			33.756

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	2.15	29.962	15878	791	99.99	0.181	0.179	0.18	0.217	0.21	RANDOM	38.842

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]
-0.44	-0.22		-0.44		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.313
r_dihedral_angle_4_deg	22.024
r_dihedral_angle_3_deg	13.633
r_dihedral_angle_1_deg	6.99
r_scangle_it	3.539
r_scbond_it	2.284
r_angle_refined_deg	1.537
r_mcangle_it	1.31
r_angle_other_deg	1.172
r_mcbond_it	0.701

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.313
r_dihedral_angle_4_deg	22.024
r_dihedral_angle_3_deg	13.633
r_dihedral_angle_1_deg	6.99
r_scangle_it	3.539
r_scbond_it	2.284
r_angle_refined_deg	1.537
r_mcangle_it	1.31
r_angle_other_deg	1.172
r_mcbond_it	0.701
r_mcbond_other	0.201
r_chiral_restr	0.095
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1392
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	87

Software

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

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.