4A64 | pdb_00004a64

Crystal structure of the N-terminal domain of human Cul4B at 2.57A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U6G	PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE
experimental model	PDB	1LDK	PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE
experimental model	PDB	1LDJ	PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE
experimental model	PDB	2HYE	PDB ENTRIES 1U6G, 1LDK, 1LDJ, 2HYE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				24% PEG4000, 100 MM LISO4, 100 MM TRIS (PH 8.2)

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.248	α = 90
b = 157.091	β = 95.71
c = 92.916	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC CCD		2011-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.57	19.97	99.7	0.06	18.6	4.2		58043		2	67

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	2.57	2.71	99.9		0.73	2	4.3

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 1U6G, 1LDK, 1LDJ, 2HYE	2.57	19.74	55064	2940	99.63	0.1866	0.18431	0.19	0.22989	0.23	RANDOM	51.113

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]
2.7		-1.54	-0.56		-2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.765
r_dihedral_angle_4_deg	20.331
r_dihedral_angle_3_deg	16.428
r_dihedral_angle_1_deg	5.142
r_angle_refined_deg	1.6
r_angle_other_deg	1.414
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_bond_other_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
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	11036
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	28

Software

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