1WDX | pdb_00001wdx

Yeast BBC1 SH3 domain, triclinic crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		atomic-resolution structure of yeast bbc1 SH3 domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	3.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	40.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.73	α = 89.83
b = 44.77	β = 83.37
c = 51.12	γ = 85.41

Symmetry
Space Group	P 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	MARRESEARCH		2004-01-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A		EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.2	20	90.8	0.144	3.9	1.7	11615	11615	-3	-3	18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.4	92.5		0.291	2.3	1.7	2707

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	atomic-resolution structure of yeast bbc1 SH3 domain	2.5	10	-3	7751	7751	388	90.26	0.26594	0.26594	0.26286	0.27	0.32595	0.33	RANDOM	10.038

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]
2.26	-0.31	-0.2	-2.06	-0.66	-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.169
r_scangle_it	0.973
r_angle_refined_deg	0.947
r_mcangle_it	0.942
r_angle_other_deg	0.705
r_scbond_it	0.654
r_mcbond_it	0.566
r_symmetry_vdw_refined	0.233
r_symmetry_vdw_other	0.198
r_nbd_other	0.195
r_nbd_refined	0.158
r_xyhbond_nbd_refined	0.14
r_nbtor_other	0.081
r_chiral_restr	0.059
r_symmetry_hbond_refined	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2068
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms

Software

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