1ZUU | pdb_00001zuu

Crystal structure of the yeast Bzz1 first SH3 domain at 0.97-A resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E6H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2	37.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.74	α = 90
b = 36.74	β = 90
c = 76.55	γ = 90

Symmetry
Space Group	P 43 21 2

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		2005-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.976	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	0.97	20	100	0.086	17.4	10.2	31881	31881	-3	-3	8.7

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)
	0.97	1	100		0.575	3.7	7.3	2730

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	1E6H	0.97	20	-3	31881	31881	1619	100	0.12407	0.12407	0.12309	0.14	0.1422	0.16	RANDOM	6.294

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]
0.22			0.22		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.456
r_dihedral_angle_3_deg	12.812
r_dihedral_angle_4_deg	11.19
r_sphericity_free	10.099
r_dihedral_angle_1_deg	7.018
r_scangle_it	4.185
r_scbond_it	3.435
r_sphericity_bonded	3.307
r_mcangle_it	2.473
r_mcbond_it	2.087
r_angle_refined_deg	1.904
r_rigid_bond_restr	1.685
r_mcbond_other	0.951
r_angle_other_deg	0.86
r_symmetry_vdw_other	0.263
r_symmetry_hbond_refined	0.262
r_xyhbond_nbd_refined	0.25
r_nbd_refined	0.211
r_nbd_other	0.186
r_symmetry_vdw_refined	0.171
r_nbtor_refined	0.165
r_chiral_restr	0.117
r_nbtor_other	0.092
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	535
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing