2Y30

Simocyclinone D8 bound form of TetR-like repressor SimR

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y2Z	PDB ENTRY 2Y2Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6		HANGING DROP VAPOUR DIFFUSION. PROTEIN AT 5MG/ML PLUS EXCESS LIGAND IN 25MM TRIS-HCL PH8.4, 300MM NACL MIXED WITH 25% PEG 1000, 0.1M SODIUM ACETATE PH4.6 IN 1 TO 1 RATIO

Crystal Properties
Matthews coefficient	Solvent content
2.33	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.37	α = 90
b = 83.91	β = 90.94
c = 45.47	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 CCD		2009-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	2.3	42.39	97	0.08	10.3	2.9		23951		-3	30.7

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	2.3	2.42	83.4		0.23	3.3	2.3

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 2Y2Z	2.3	73.68	22723	1227	96.94	0.20326	0.19966	0.2	0.27001	0.26	RANDOM	20.6

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]
-1.59		-1.26	1.42		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.245
r_dihedral_angle_4_deg	16.563
r_dihedral_angle_3_deg	16.257
r_dihedral_angle_1_deg	5.725
r_scangle_it	3.424
r_scbond_it	2.132
r_angle_refined_deg	1.459
r_mcangle_it	1.382
r_angle_other_deg	0.903
r_mcbond_it	0.748
r_chiral_restr	0.293
r_mcbond_other	0.156
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_gen_planes_other	0.009
r_bond_other_d	0.003
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_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	3564
Nucleic Acid Atoms
Solvent Atoms	164
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing