1OOT

Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein at 1.39 A resolution

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	7.5	295	70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.93	α = 90
b = 39.93	β = 90
c = 69.49	γ = 120

Symmetry
Space Group	P 31 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	MARRESEARCH		2003-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8028	EMBL/DESY, HAMBURG	X13

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	1.38	30	97	0.056	15	5.5	13185	13185		-3	21.65

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)
	1.38	1.44	88.1		0.414	2.7	3.1	1398

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 (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	1SEM	1.39	20	13120	13120	656	97.76	0.13397	0.13397	0.13207	0.14	0.17046	0.17	RANDOM	15.044

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]
1.17	0.58		1.17		-1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	7.14
r_scangle_it	5.918
r_dihedral_angle_1_deg	5.179
r_sphericity_bonded	5.126
r_mcangle_it	4.075
r_scbond_it	3.992
r_mcbond_it	2.991
r_rigid_bond_restr	2.246
r_angle_refined_deg	1.842
r_angle_other_deg	0.879
r_symmetry_vdw_other	0.366
r_symmetry_hbond_refined	0.258
r_nbd_other	0.246
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.19
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.114
r_nbtor_other	0.09
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	515
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	3

Software

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