2VAC | pdb_00002vac

Structure of N-terminal Actin Depolymerizing Factor homology (ADF-H) domain of human twinfilin-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M4J	PDB ENTRY 1M4J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		0.01M ZINC CHLORIDE,10% ETHYLENE GLYCOL,20% PEG6000, 0.1M TRIS PH8.0

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.817	α = 90
b = 48.56	β = 90
c = 70.127	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	IMAGE PLATE	RIGAKU IMAGE PLATE	MULTI-LAYER VARIMAX HR	2007-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E

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	1.7	20.1	97.5	0.07	24.4	6.8		13653			18.66

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	1.7	1.79	94.9		0.54	2.5	6.6

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 1M4J	1.7	20	12971	678	97.2	0.172	0.17	0.18	0.214	0.23	RANDOM	15.83

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]
-0.31			-0.72		1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.356
r_dihedral_angle_4_deg	15.983
r_dihedral_angle_3_deg	11.424
r_dihedral_angle_1_deg	6.275
r_scangle_it	6.23
r_scbond_it	5.001
r_mcangle_it	2.978
r_mcbond_it	2.775
r_angle_other_deg	1.811
r_angle_refined_deg	1.29
r_symmetry_vdw_other	0.302
r_nbd_refined	0.208
r_nbd_other	0.199
r_symmetry_vdw_refined	0.18
r_nbtor_refined	0.173
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.123
r_nbtor_other	0.096
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
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	1065
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	7

Software

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