2BKI | pdb_00002bki

Myosin VI nucleotide-free (MDinsert2-IQ) 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
3.91	68.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.781	α = 90
b = 250.167	β = 90
c = 67.274	γ = 90

Symmetry
Space Group	P 21 21 2

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 ID23-1		ESRF	ID23-1

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	2.9	40	97	0.12	16.3	6.3		38961		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	2.9	3.06	97		0.44	3.7

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	2.9	40	36191	1948	95	0.266	0.264	0.24	0.304	0.29	RANDOM	43.74

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]
-2.74			2.65		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.238
r_angle_other_deg	2.037
r_scangle_it	1.987
r_angle_refined_deg	1.149
r_scbond_it	1.129
r_mcangle_it	0.965
r_mcbond_it	0.517
r_symmetry_vdw_other	0.226
r_nbd_other	0.207
r_symmetry_hbond_refined	0.202
r_nbd_refined	0.174
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_refined	0.164
r_nbtor_other	0.081
r_chiral_restr	0.064
r_bond_refined_d	0.013
r_gen_planes_refined	0.003
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	7991
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	9

Software

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