3DI5 | pdb_00003di5

Crystal structure of a dinb-like protein (bce_4655) from bacillus cereus atcc 10987 at 2.01 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.57	293	0.2M magnesium chloride, 30.5% polyethylene glycol 4000, 0.1M TRIS pH 8.57, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.12	α = 90
b = 84.19	β = 90
c = 50.32	γ = 90

Symmetry
Space Group	C 2 2 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)	2008-04-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97916,0.97860	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	2.009	28.63	95.6	0.034	13.57	3.93		11180		-3	35.693

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	2.07	77.6		0.413	2.63

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	2.009	28.63	11168	534	97.98	0.231	0.229	0.23	0.266	0.25	RANDOM	33.148

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]
-4.4			5.29		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.434
r_dihedral_angle_4_deg	23.366
r_dihedral_angle_3_deg	13.892
r_dihedral_angle_1_deg	5.035
r_scangle_it	2.259
r_scbond_it	1.641
r_angle_refined_deg	1.273
r_mcangle_it	1.147
r_angle_other_deg	0.924
r_mcbond_it	0.764
r_nbd_refined	0.221
r_nbtor_refined	0.181
r_nbd_other	0.17
r_mcbond_other	0.154
r_xyhbond_nbd_refined	0.15
r_symmetry_vdw_refined	0.147
r_symmetry_vdw_other	0.121
r_nbtor_other	0.088
r_chiral_restr	0.076
r_symmetry_hbond_refined	0.076
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1146
Nucleic Acid Atoms
Solvent Atoms	55
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
SHELXD	phasing
autoSHARP	phasing