3U23 | pdb_00003u23

Atomic resolution crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide from human RIN3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G6F	pdb entries 2G6F, 1OEB, 2AK5, 2FEI, 3IQL
experimental model	PDB	1OEB	pdb entries 2G6F, 1OEB, 2AK5, 2FEI, 3IQL
experimental model	PDB	2AK5	pdb entries 2G6F, 1OEB, 2AK5, 2FEI, 3IQL
experimental model	PDB	2FEI	pdb entries 2G6F, 1OEB, 2AK5, 2FEI, 3IQL
experimental model	PDB	3IQL	pdb entries 2G6F, 1OEB, 2AK5, 2FEI, 3IQL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	0.1 M HEPES pH 7.5, 1.4 M tri-sodium citrate dihydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.13	α = 90
b = 32.04	β = 92.56
c = 39.18	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	PIXEL	PSI PILATUS 6M		2011-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	1.11	27.43	92.8	0.056	14.98	6	26161	24275	-3	-3	13.68

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	1.11	1.14	59.9		0.521	2.24	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 2G6F, 1OEB, 2AK5, 2FEI, 3IQL	1.11	27.43	26161	23056	1217	92.79	0.15151	0.15071	0.16	0.16663	0.17	RANDOM	15.91

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]
1.75		-0.17	-0.91		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.621
r_dihedral_angle_4_deg	15.098
r_dihedral_angle_3_deg	13.379
r_scangle_it	8.198
r_dihedral_angle_1_deg	6.383
r_scbond_it	5.223
r_mcangle_it	3.85
r_mcbond_it	2.519
r_angle_refined_deg	2.271
r_rigid_bond_restr	2.112
r_angle_other_deg	1.586
r_mcbond_other	0.794
r_chiral_restr	0.136
r_bond_refined_d	0.025
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	562
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	4

Software

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