3SNH | pdb_00003snh

Crystal structure of nucleotide-free human dynamin1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AKA	PDB ENTRIES 2AKA, 2DYN and 3LJB
experimental model	PDB	2DYN	PDB ENTRIES 2AKA, 2DYN and 3LJB
experimental model	PDB	3LJB	PDB ENTRIES 2AKA, 2DYN and 3LJB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	277	9% PEG400, 6% isopropanol, 100 mM HEPES/NaOH (pH 7.3), 10 mM MgCl2, 10 mM KCl. , VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.056	α = 90
b = 201.993	β = 90
c = 59.016	γ = 90

Symmetry
Space Group	C 2 2 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	RAYONIX MX-225	MIRROR	2010-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.7	35	99.2	0.076	13.1	4	10295	10214	-3		111

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.7	3.8	99.7		0.665	2.14	4	717

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 ENTRIES 2AKA, 2DYN and 3LJB	3.7	32.59	10214	487	99.44	0.2903	0.2882	0.2871	0.3305	0.3038	RANDOM	176.8996

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]
7.18			-8.74		1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.023
r_dihedral_angle_4_deg	18.125
r_dihedral_angle_3_deg	17.204
r_dihedral_angle_1_deg	3.237
r_angle_refined_deg	0.982
r_angle_other_deg	0.853
r_chiral_restr	0.06
r_bond_refined_d	0.007
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5285
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction