6G35 | pdb_00006g35

Crystal structure of haspin in complex with 5-bromotubercidin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OUC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	51-63% MPD and 0.1M SPG buffer, pH 6.0-6.5

Crystal Properties
Matthews coefficient	Solvent content
3	59.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.301	α = 90
b = 78.76	β = 90
c = 79.3	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	PIXEL	DECTRIS PILATUS3 6M		2015-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.55	23.87	99.8	0.073	0.996	10.8	5.2		71557

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.63	99.8		0.643	0.758	2.3	5.2

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	4OUC	1.55	23.87	67910	3573	99.61	0.16128	0.1602	0.17	0.18269	0.19	RANDOM	28.455

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]
-1.23			0.46		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.336
r_sphericity_bonded	25.5
r_dihedral_angle_4_deg	13.766
r_dihedral_angle_3_deg	12.414
r_long_range_B_refined	7.082
r_long_range_B_other	7.081
r_dihedral_angle_1_deg	6.542
r_scangle_other	2.357
r_scbond_it	1.622
r_scbond_other	1.622
r_angle_refined_deg	1.615
r_mcangle_it	1.301
r_mcangle_other	1.3
r_angle_other_deg	0.934
r_mcbond_it	0.812
r_mcbond_other	0.811
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2699
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing