3IQL | pdb_00003iql

Crystal structure of the rat endophilin-A1 SH3 domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GCQ	PDB entry 1GCQ, chain A, Non-conserved residue pruned to CB atom using CHAINSAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	277	20% methyl-2,4-pentanediol, 0.1M sodium acetate, 0.05M calcium chloride, 10mM 2-mercaptoethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.338	α = 90
b = 34.156	β = 107.79
c = 62.729	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	ADSC QUANTUM 4		2007-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.97720	CHESS	A1

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	1.4	30	96.3	0.031	30.2	3	24510	23667		2	8.5

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)
	1.4	1.5	85.5		0.071	11.1	1.9	4701

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 entry 1GCQ, chain A, Non-conserved residue pruned to CB atom using CHAINSAW	1.4	30	24901	23667	1234	96.56	0.12837	0.12702	0.13	0.15358	0.16	RANDOM	13.739

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		0.14	-0.27		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.769
r_dihedral_angle_4_deg	22.324
r_dihedral_angle_3_deg	13.004
r_dihedral_angle_1_deg	6.311
r_sphericity_free	6.116
r_scangle_it	3.908
r_sphericity_bonded	3.734
r_scbond_it	3.697
r_rigid_bond_restr	3.433
r_mcangle_it	2.004
r_mcbond_it	1.405
r_angle_refined_deg	1.402
r_nbtor_refined	0.322
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.193
r_symmetry_vdw_refined	0.18
r_symmetry_hbond_refined	0.173
r_chiral_restr	0.102
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1174
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	2

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling