2IKQ | pdb_00002ikq

Crystal structure of mouse Sts-1 PGM domain in complex with phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H0Q	PDB entry 1H0Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	14% PEG 8000, 0.1 M HEPES, 0.3 M Na Acetate, 0.2 M Na/K phosphate, pH 7.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.96	α = 90
b = 74.671	β = 100.79
c = 101.279	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	ADSC QUANTUM 210		2006-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.0	NSLS	X26C

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	2.609	100	98	0.63	0.63	30	4.1	25668	25668		2	74.8

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	2.609	2.69	99.5		0.556	0.556	3.2	4.2	2582

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1H0Q	2.609	99.5	25664	24371	1293	97.58	0.2491	0.24773	0.31	0.27515	0.33	RANDOM	68.359

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]
-4.21		-1.42	8.82		-5.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.681
r_dihedral_angle_4_deg	20.943
r_dihedral_angle_3_deg	19.431
r_dihedral_angle_1_deg	6.359
r_scangle_it	2.312
r_scbond_it	1.494
r_angle_refined_deg	1.42
r_mcangle_it	1.294
r_mcbond_it	0.707
r_symmetry_hbond_refined	0.43
r_symmetry_vdw_refined	0.367
r_nbtor_refined	0.315
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6103
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	15

Software

Software
Software Name	Purpose
HKL-2000	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing