5K26 | pdb_00005k26

Structure of the SH3 domain of MLK3 bound to peptide generated from phage display

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SEM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1 M Na-Phosphate, 0.1 M K-Phosphate, 0.1 M MES 6.5, 1.5 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.31	48.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64	α = 90
b = 64	β = 90
c = 35.2	γ = 120

Symmetry
Space Group	P 31

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	MARMOSAIC 225 mm CCD		2015-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.978720	APS	21-ID-F

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	1.2	55.43	97.2	0.042	19.53	4.92		48242

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	1.2	1.27	83.1		0.418	2.76	2.55

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	1SEM	1.2	55.43	46672	2412	97.21	0.13865	0.13712	0.15	0.16826	0.17	RANDOM	21.026

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]
-0.54	-0.27		-0.54		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.606
r_sphericity_free	32.597
r_sphericity_bonded	21.62
r_dihedral_angle_4_deg	20.048
r_dihedral_angle_3_deg	12.764
r_scangle_other	11.004
r_long_range_B_refined	9.85
r_long_range_B_other	9.847
r_scbond_other	7.901
r_scbond_it	7.9
r_rigid_bond_restr	7.214
r_dihedral_angle_1_deg	6.022
r_mcangle_other	4.326
r_mcangle_it	4.308
r_mcbond_it	3.475
r_mcbond_other	3.459
r_angle_refined_deg	3.006
r_angle_other_deg	1.585
r_chiral_restr	0.178
r_bond_refined_d	0.035
r_gen_planes_refined	0.016
r_gen_planes_other	0.008
r_bond_other_d	0.005
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1161
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing