1W9K | pdb_00001w9k

Dictyostelium discoideum Myosin II motor domain S456E with bound MgADP-BeFx

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		10% PEG 8000, 50 MM HEPES PH 7, 100 MM NACL, 2 MM DTT, 2 MM NAN3 BY MICROSEEDING

Crystal Properties
Matthews coefficient	Solvent content
3	58.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.704	α = 90
b = 179.428	β = 90
c = 54.153	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	IMAGE PLATE	MARRESEARCH		2000-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	40	96	0.06	24	6.2		68455		3

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	2.05	2.1	96.2		0.26	4.3	5.2

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 1MMA	2.05	40	60609	3179	98.1	0.2	0.198	0.21	0.232	0.24	RANDOM	33.58

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]
-0.48			0.87		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.497
r_dihedral_angle_1_deg	3.808
r_scangle_it	3.402
r_mcangle_it	3.099
r_scbond_it	2.167
r_mcbond_it	1.949
r_angle_refined_deg	1.407
r_angle_other_deg	0.853
r_symmetry_hbond_refined	0.234
r_nbd_refined	0.231
r_nbd_other	0.208
r_symmetry_vdw_refined	0.204
r_xyhbond_nbd_refined	0.183
r_symmetry_vdw_other	0.141
r_chiral_restr	0.126
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_nbtor_other
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	5591
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing