2ODA | pdb_00002oda

Crystal Structure of PSPTO_2114

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	277	15-20% PEG 3350, 150-200mM Sodium formate, 100mM Hepes pH 7.3, 5mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.612	α = 90
b = 74.427	β = 90
c = 106.354	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 210		2005-11-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X12C	0.97980, 0.97786, 0.95000	NSLS	X12C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	60	98	0.065	41	11	30874	30874			13.45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.97	83.8		0.183	7.3	6.6	2580

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.9	43.27	30590	3024	97.48	0.172	0.167	0.1731	0.219	0.1797	RANDOM	13.815

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]
0.31			0.1		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.338
r_dihedral_angle_4_deg	13.394
r_dihedral_angle_3_deg	12.802
r_dihedral_angle_1_deg	5.62
r_scangle_it	2.999
r_scbond_it	2.034
r_angle_refined_deg	1.354
r_mcangle_it	1.188
r_mcbond_it	0.93
r_nbtor_refined	0.295
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.189
r_symmetry_hbond_refined	0.152
r_xyhbond_nbd_refined	0.149
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2879
Nucleic Acid Atoms
Solvent Atoms	535
Heterogen Atoms	31

Software

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