2BKH | pdb_00002bkh

Myosin VI nucleotide-free (MDInsert2) crystal structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OE9	PDB ENTRY 1OE9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				8-10% PEG 8000, 50MM MES PH 6.7, 150MM NH4.SO4, 3% ISO-PROPANOL, 3% TERT-BUTANOL

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.57	α = 90
b = 104.437	β = 91.26
c = 90.284	γ = 90

Symmetry
Space Group	P 1 21 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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.4	40	99.8	0.09	14.4	4		49721		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	2.4	2.49	99.9		0.42	3.2

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 1OE9	2.4	40	47177	2520	99.8	0.208	0.206	0.21	0.254	0.25	RANDOM	45.1

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]
0.62		-0.09	-1.2		0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.683
r_scangle_it	2.653
r_scbond_it	1.512
r_mcangle_it	1.179
r_angle_refined_deg	1.158
r_angle_other_deg	0.776
r_mcbond_it	0.617
r_symmetry_vdw_other	0.262
r_nbd_other	0.223
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.181
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.114
r_nbtor_other	0.084
r_chiral_restr	0.065
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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	7403
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing