2RCD | pdb_00002rcd

CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3225 FAMILY (ECA3500) FROM PECTOBACTERIUM ATROSEPTICUM SCRI1043 AT 2.32 A RESOLUTION

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	NANODROP, 1.1M Lithium chloride, 24.0% PEG 6000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.62	52.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.375	α = 90
b = 93.524	β = 105.32
c = 72.919	γ = 90

Symmetry
Space Group	C 1 2 1

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)	2007-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97898	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	2.32	29.463	97.7	0.108	0.108	6	3.2		25597			38.72

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	2.32	2.38	97		0.639	0.639	1.1	3.2	1891

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	SAD	THROUGHOUT	2.32	29.463	25596	1291	97.53	0.19	0.187	0.2	0.242	0.25	RANDOM	43.889

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]
-1.15		0.93	-3.3		4.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.277
r_dihedral_angle_4_deg	13.951
r_dihedral_angle_3_deg	12.051
r_scangle_it	5.854
r_scbond_it	4.686
r_dihedral_angle_1_deg	3.28
r_mcangle_it	2.298
r_mcbond_it	1.635
r_angle_refined_deg	1.535
r_angle_other_deg	1.029
r_mcbond_other	0.448
r_symmetry_vdw_other	0.285
r_nbd_refined	0.19
r_nbd_other	0.185
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.178
r_symmetry_vdw_refined	0.128
r_symmetry_hbond_refined	0.111
r_chiral_restr	0.094
r_nbtor_other	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3969
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	4

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