2OBP | pdb_00002obp

Crystal structure of a putative dna-binding protein (reut_b4095) from ralstonia eutropha jmp134 at 1.70 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	5.8	277	0.2M MgNO3, 20.0% PEG-3350, No Buffer pH 5.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.58	α = 90
b = 76.58	β = 90
c = 137.86	γ = 120

Symmetry
Space Group	P 63 2 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)	2006-12-03	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97932, 0.97910	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	1.7	29.412	98.2	0.063	19.02			26996			30.103

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	1.7	1.76	90.9		0.628	3.1		4479

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	1.7	29.412	26956	1351	99.71	0.188	0.186	0.19	0.219	0.22	RANDOM	20.67

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]
1.06	0.53		1.06		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.266
r_dihedral_angle_4_deg	19.184
r_dihedral_angle_3_deg	12.018
r_scangle_it	5.665
r_dihedral_angle_1_deg	5.55
r_scbond_it	4.335
r_mcangle_it	2.397
r_mcbond_it	1.927
r_angle_refined_deg	1.511
r_angle_other_deg	1.009
r_mcbond_other	0.636
r_xyhbond_nbd_other	0.225
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.218
r_xyhbond_nbd_refined	0.208
r_symmetry_vdw_refined	0.202
r_symmetry_vdw_other	0.198
r_nbd_other	0.195
r_nbtor_refined	0.173
r_chiral_restr	0.097
r_nbtor_other	0.088
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1177
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	5

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
SOLVE	phasing