4C9Z | pdb_00004c9z

Crystal structure of Siah1 at 1.95 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A25	PDB ENTRY 2A25

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				CRYSTALS GREW FROM EQUAL VOLUMES OF PROTEIN SOLUTION (15 MG ML-1 IN 15 MM TRIS-HCL PH7.5, 30 MM NACL AND 10 MM DTT) AND RESERVOIR SOLUTION (100 MES PH6.5, 1.5 M MGSO4).

Crystal Properties
Matthews coefficient	Solvent content
2.99	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.14	α = 90
b = 104.59	β = 90
c = 133.16	γ = 90

Symmetry
Space Group	I 2 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	287	IMAGE PLATE	RIGAKU RAXIS IV		2011-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	1.95	44.99	99.3	0.04	19.3	3.7		38340		2

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	1.95	2.06	96		0.18	4.5	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2A25	1.95	40	36417	1918	99.27	0.19967	0.19761	0.22	0.23855	0.26	RANDOM	42.28

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]
-0.2			0.55		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.793
r_dihedral_angle_3_deg	15.277
r_dihedral_angle_4_deg	10.572
r_scangle_it	7.837
r_scbond_it	5.572
r_dihedral_angle_1_deg	5.568
r_mcangle_it	3.539
r_mcbond_it	2.345
r_angle_refined_deg	1.302
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3002
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing