3GRD | pdb_00003grd

Crystal structure of NTF2-superfamily protein with unknown function (NP_977240.1) from BACILLUS CEREUS ATCC 10987 at 1.25 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.29	277	33.8000% polyethylene glycol 4000, 0.2000M sodium acetate, 0.1M TRIS pH 8.29, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.09	α = 90
b = 47.14	β = 90
c = 151.79	γ = 90

Symmetry
Space Group	P 21 21 21

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)	2008-11-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162,0.97862	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	1.25	29.566	96.1	0.041	11.63			81747		-3	10.01

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)
	1.25	1.29	82.5		0.469	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	MAD	THROUGHOUT	1.25	29.566	81659	4091	98.96	0.135	0.133	0.14	0.167	0.17	RANDOM	13.625

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]
0.08			0.12		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.722
r_dihedral_angle_4_deg	13.478
r_dihedral_angle_3_deg	11.095
r_sphericity_free	9.093
r_dihedral_angle_1_deg	6.203
r_scangle_it	6.066
r_scbond_it	4.543
r_sphericity_bonded	4.436
r_mcangle_it	3.164
r_mcbond_it	2.362
r_rigid_bond_restr	1.991
r_mcbond_other	1.648
r_angle_refined_deg	1.54
r_angle_other_deg	0.893
r_nbd_refined	0.267
r_symmetry_vdw_refined	0.265
r_symmetry_vdw_other	0.224
r_symmetry_hbond_refined	0.192
r_nbd_other	0.191
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.102
r_nbtor_other	0.088
r_metal_ion_refined	0.055
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2350
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	18

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