2RE3 | pdb_00002re3

CRYSTAL STRUCTURE OF a DUF1285 family protein (SPO_0140) FROM SILICIBACTER POMEROYI DSS-3 AT 2.50 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	NANODROP, 20.0% Ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3	59.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.37	α = 90
b = 75.37	β = 90
c = 182.687	γ = 90

Symmetry
Space Group	P 43 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 325 mm CCD	Flat mirror (vertical focusing)	2007-05-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97908, 0.97935	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	29.488	99.9	0.129	0.129	4.9	7.4		19038

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.56	100		0.76	0.76	1	7.6	1357

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	2.5	29.488	18959	972	99.73	0.217	0.215	0.22	0.258	0.26	RANDOM	25.385

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]
0.92			0.92		-1.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.295
r_dihedral_angle_4_deg	22.427
r_dihedral_angle_3_deg	17.08
r_dihedral_angle_1_deg	6.781
r_scangle_it	4.322
r_scbond_it	3.511
r_mcangle_it	2.937
r_mcbond_it	1.875
r_angle_refined_deg	1.557
r_angle_other_deg	0.929
r_mcbond_other	0.446
r_symmetry_vdw_other	0.239
r_nbd_other	0.209
r_nbd_refined	0.205
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.091
r_nbtor_other	0.088
r_symmetry_vdw_refined	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2840
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHARP	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction