3BT5 | pdb_00003bt5

Crystal structure of DUF305 fragment from Deinococcus radiodurans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QF9	PDB entry 2QF9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	0.1M Bis-Tris pH 5.5, 3M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.69	α = 90
b = 49.69	β = 90
c = 71.191	γ = 90

Symmetry
Space Group	P 41

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	MAR CCD 165 mm		2007-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97930	APS	31-ID

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	1.35	50	99.7	0.042	9.9	7.2	37848	37848

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)
	1.35	1.4	100		0.655		7	3775

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2QF9	1.35	25.01	37810	37810	1914	99.71	0.156	0.156	0.154	0.15	0.188	0.18	RANDOM	23.942

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]
0.01			0.01		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.091
r_sphericity_free	16.551
r_dihedral_angle_4_deg	14.184
r_dihedral_angle_3_deg	13.488
r_sphericity_bonded	10.143
r_scangle_it	7.508
r_scbond_it	5.354
r_mcangle_it	5.051
r_dihedral_angle_1_deg	4.174
r_mcbond_it	4.08
r_rigid_bond_restr	3.908
r_angle_refined_deg	1.328
r_nbtor_refined	0.31
r_nbd_refined	0.223
r_symmetry_hbond_refined	0.202
r_symmetry_vdw_refined	0.19
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1282
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing