7LBK

Crystal structure of human Survivin bound to histone H3 T3phK4me3 peptide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	The crystal was obtained by mixing 1 uL of protein at 10 mg/mL with 1 uL of mother liquor composed of 0.16 M potassium/sodium tartrate, 14% PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.292	α = 90
b = 71.369	β = 129.33
c = 82.554	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	CCD	RAYONIX MX-300		2013-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.27822	APS	21-ID-D

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	2.7	50	98.1	0.094	11.5	14.8		13890

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	2.7	2.75	93		0.756		11.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.7	41.04	11791	623	87.2	0.214	0.212	0.253	RANDOM	40.61

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]
-1.44		-0.17	2.03		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.452
r_dihedral_angle_4_deg	21.838
r_dihedral_angle_3_deg	17.743
r_dihedral_angle_1_deg	5.576
r_angle_refined_deg	1.699
r_angle_other_deg	1.051
r_chiral_restr	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.004
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	2250
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
SCALEPACK	data scaling
HKL-3000	data reduction
SHELXD	phasing
DM	phasing
MLPHARE	phasing
HKL-3000	phasing
BUCCANEER	model building
PDB_EXTRACT	data extraction