3MN5 | pdb_00003mn5

Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	277	0.2 Magnesium formate pH 5.9 20% PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.96	α = 90
b = 71.81	β = 90
c = 100.72	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	MAR CCD 165 mm	LN2 cooled fixed-exit Si(111) monochromator	2009-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9801	SLS	X10SA

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	1.5	50	79	0.049			62290	49209	2	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)
	1.5	1.6	38.1		0.203	4.4

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	1NWK	1.5	39.25	46688	2511	79.04	0.17386	0.17164	0.17	0.216	0.21	RANDOM	19.832

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]
-0.34			-0.06		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.952
r_dihedral_angle_4_deg	21.669
r_dihedral_angle_3_deg	15.76
r_dihedral_angle_1_deg	11.942
r_scangle_it	5.606
r_scbond_it	3.628
r_angle_refined_deg	2.403
r_mcangle_it	2.389
r_mcbond_it	1.459
r_chiral_restr	0.382

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.952
r_dihedral_angle_4_deg	21.669
r_dihedral_angle_3_deg	15.76
r_dihedral_angle_1_deg	11.942
r_scangle_it	5.606
r_scbond_it	3.628
r_angle_refined_deg	2.403
r_mcangle_it	2.389
r_mcbond_it	1.459
r_chiral_restr	0.382
r_bond_refined_d	0.027
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2870
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	59

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.