2OU6 | pdb_00002ou6

Crystal structure of a putative metalloenzyme of the duf664 family (dr_1065) from deinococcus radiodurans at 1.80 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	NANODROP, 1.6M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.933	α = 90
b = 57.933	β = 90
c = 250.773	γ = 120

Symmetry
Space Group	P 65 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)	2007-02-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97905, 0.97932, 0.91837	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	1.8	125	91.1	0.07	0.07	7.1	6.9		22207			21.72

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	1.8	1.85	61.4		0.268	0.268	2.5	2.6	1047

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 (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	MAD	THROUGHOUT	1.8	125	22101	1137	91.06	0.157	0.157	0.155	0.17	0.188	0.19	RANDOM	19.024

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]
-1.32	-0.66		-1.32		1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.358
r_dihedral_angle_4_deg	15.484
r_dihedral_angle_3_deg	11.829
r_scangle_it	6.492
r_dihedral_angle_1_deg	5.626
r_scbond_it	4.621
r_mcangle_it	2.609
r_mcbond_it	2.02
r_angle_refined_deg	1.548
r_angle_other_deg	0.912
r_mcbond_other	0.505
r_symmetry_vdw_other	0.303
r_nbd_refined	0.217
r_nbd_other	0.185
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.161
r_symmetry_vdw_refined	0.136
r_chiral_restr	0.102
r_symmetry_hbond_refined	0.089
r_nbtor_other	0.087
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1428
Nucleic Acid Atoms
Solvent Atoms	266
Heterogen Atoms	23

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing