2VTB

Structure of cryptochrome 3 - DNA complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J4D	PDB ENTRY 2J4D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		10 MG/ML PROTEIN, 85 MM NA-CITRATE PH 4.6, 170 MM NH4-ACETATE, 21.5% (W/V) PEG 4000 AND 15% (V/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.734	α = 90
b = 136.082	β = 90
c = 211.484	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	MARRESEARCH	MIRRORS	2007-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A		EMBL/DESY, HAMBURG	BW7A

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	15.1	99.2	0.1	14.9	6.02		229217		-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	2.05	89.6		0.41	2.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2J4D	2.01	15.03	227588	1518	99.2	0.185	0.184	0.222	RANDOM	35.98

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]
-0.08			-0.02		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.206
r_dihedral_angle_4_deg	18.282
r_dihedral_angle_3_deg	12.852
r_dihedral_angle_1_deg	5.451
r_scangle_it	1.622
r_angle_refined_deg	1.151
r_scbond_it	1.014
r_angle_other_deg	0.867
r_mcangle_it	0.8
r_mcbond_it	0.471
r_symmetry_vdw_refined	0.246
r_symmetry_vdw_other	0.217
r_nbd_refined	0.197
r_nbd_other	0.183
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.131
r_nbtor_other	0.079
r_chiral_restr	0.072
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
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	23956
Nucleic Acid Atoms	520
Solvent Atoms	1305
Heterogen Atoms	528

Software

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