3A5L | pdb_00003a5l

Crystal Structure of a Dictyostelium P109A Mg2+-Actin in Complex with Human Gelsolin Segment 1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A5N	PDB ENTRY 3A5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.852	α = 90
b = 69.005	β = 90
c = 180.881	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	100	CCD	ADSC QUANTUM 315		2008-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.00000	Photon Factory	BL-5A

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	2.39	50		0.072				28588			35

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)
	2.39	2.49			0.123	13.92

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 3A5N	2.4	48.13	28410	1432	99.4	0.19	0.189	0.2	0.207	0.21	RANDOM	37.333

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]
0.86			-2.29		1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.476
r_dihedral_angle_4_deg	28.716
r_dihedral_angle_3_deg	18.486
r_dihedral_angle_1_deg	6.1
r_scangle_it	5.097
r_scbond_it	3.792
r_mcangle_it	2.271
r_angle_refined_deg	2.007
r_mcbond_it	1.588
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.476
r_dihedral_angle_4_deg	28.716
r_dihedral_angle_3_deg	18.486
r_dihedral_angle_1_deg	6.1
r_scangle_it	5.097
r_scbond_it	3.792
r_mcangle_it	2.271
r_angle_refined_deg	2.007
r_mcbond_it	1.588
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.316
r_symmetry_vdw_refined	0.246
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.21
r_metal_ion_refined	0.135
r_chiral_restr	0.12
r_bond_refined_d	0.018
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3790
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.