5L23

Crystal structure of the complex between the N-terminal SH3 domain of CrkII and a proline-rich ligand

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		286	Lithium sulfate monohydrate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.86	34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.6	α = 90
b = 41.34	β = 90
c = 56.82	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	113	IMAGE PLATE	RIGAKU		2015-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	1.77	33.43	100	0.16	0.977	11.7	7.4		6759

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	1.77	1.87	99.9		0.2	0.96	8.4	7.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1cka	1.77	33.43	6462	264	99.96	0.17587	0.17439	0.21037	RANDOM	13.616

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]
0.11			0.07		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.067
r_dihedral_angle_3_deg	14.641
r_dihedral_angle_4_deg	11.588
r_long_range_B_other	6.781
r_long_range_B_refined	6.769
r_dihedral_angle_1_deg	5.509
r_scangle_other	4.204
r_angle_other_deg	3.556
r_scbond_it	2.708
r_scbond_other	2.708
r_angle_refined_deg	2.611
r_mcangle_other	2.564
r_mcangle_it	2.56
r_mcbond_it	1.66
r_mcbond_other	1.544
r_chiral_restr	0.138
r_bond_refined_d	0.029
r_gen_planes_other	0.028
r_gen_planes_refined	0.012
r_bond_other_d
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
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	616
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	11

Software

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