2OZJ | pdb_00002ozj

CRYSTAL STRUCTURE OF A CUPIN SUPERFAMILY PROTEIN (DSY2733) FROM DESULFITOBACTERIUM HAFNIENSE DCB-2 AT 1.60 A RESOLUTION

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	NANODROP, 0.25M Sodium chloride, 33.0% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.93	α = 90
b = 69.79	β = 90
c = 150.52	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)	2007-01-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97941, 0.97917	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	1.6	28.88	99.3	0.045	14.16	7.2		28987			22.8

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	1.6	1.66	97.3	97.3	0.675	2.1

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	1.6	28.88	28943	1475	99.53	0.18374	0.1822	0.19	0.21269	0.22	RANDOM	15.049

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]
0.29			1.37		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.489
r_dihedral_angle_4_deg	21.374
r_dihedral_angle_3_deg	14.455
r_dihedral_angle_1_deg	8.183
r_scangle_it	7.412
r_scbond_it	5.047
r_mcangle_it	3.137
r_mcbond_it	2.3
r_angle_refined_deg	1.748
r_angle_other_deg	0.966
r_mcbond_other	0.739
r_symmetry_vdw_other	0.292
r_symmetry_vdw_refined	0.283
r_nbd_refined	0.217
r_nbd_other	0.203
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.169
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.093
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other	0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1674
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MolProbity	model building
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHARP	phasing