3BZ7 | pdb_00003bz7

Crystal Structures of (S)-(-)-Blebbistatin Analogs bound to Dictyostelium discoideum myosin II

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YV3	PDB entry 1YV3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	278	mixing 5 ul of protein with an equal volume of well solution containing 100 mM MOPS, 250 mM MgCl2, 12% PEG 8000, 1 mM TCEP, and 2 mM Thymol, pH 7.0, vapor diffusion, hanging drop, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.219	α = 90
b = 146	β = 90
c = 153.086	γ = 90

Symmetry
Space Group	C 2 2 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	MAR CCD 165 mm		2005-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID	1.0	APS	32-ID

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	50	99.9	0.071	10.3	5.3		66674

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)
	2	2.07	99.7		0.234		4.8

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 1YV3	2	35.51	63262	3376	99.8	0.18502	0.18301	0.18	0.22289	0.22	RANDOM	25.469

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]
0.8			0.23		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.696
r_dihedral_angle_4_deg	14.111
r_dihedral_angle_3_deg	13.269
r_dihedral_angle_1_deg	5.66
r_scangle_it	3.49
r_scbond_it	2.348
r_mcangle_it	1.541
r_angle_refined_deg	1.39
r_mcbond_it	0.952
r_symmetry_hbond_refined	0.312
r_nbtor_refined	0.305
r_metal_ion_refined	0.302
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5546
Nucleic Acid Atoms
Solvent Atoms	658
Heterogen Atoms	56

Software

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