5IP4 | pdb_00005ip4

X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X1O	ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental model	PDB	2X1P	ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental model	PDB	2X6M	ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental model	PDB	3DWT	ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental model	PDB	3EAK	ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental model	PDB	3G9A	ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G
experimental model	PDB	3P0G	ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	20% PEGMME, 100 mM Bis-Tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.84	α = 90
b = 86.191	β = 123
c = 73.267	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2011-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.81	44.77	99.8	0.067	0.077	10.33	3.42		42622

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.81	1.9	99.7		1.1	1.27	3.28

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	ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, AND 3P0G	1.81	44.77	38934	2063	95.95	0.1967	0.19398	0.19	0.24635	0.24	RANDOM	31.575

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]
0.83		0.46	-0.37		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.236
r_dihedral_angle_4_deg	25.687
r_dihedral_angle_3_deg	16.083
r_dihedral_angle_1_deg	6.528
r_angle_refined_deg	2.121
r_chiral_restr	0.152
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	2986
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
SADABS	data scaling
REFMAC	refinement
PHASER	phasing