3GRE | pdb_00003gre

Crystal structure of Saccharomyces cerevisiae Vps15 WD repeat domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	macroseeding into microbatch	6.5	291	0.7 M ammonium malonate, 0.05 M sodium acetate, 2% 2-propanol, pH 6.5, macroseeding into microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.493	α = 90
b = 85.493	β = 90
c = 132.821	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	MARMOSAIC 300 mm CCD		2007-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

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	1.8	50	96.5	0.081	36.003	10.2	50964	50964		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	71.2		0.527	0.527	1.6	6.8	3714

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.8	49.44	50917	50917	2592	96.49	0.211	0.211	0.209	0.2037	0.246	0.2374	RANDOM	35.727

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]
1.72	0.86		1.72		-2.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.354
r_dihedral_angle_4_deg	15.775
r_dihedral_angle_3_deg	15.051
r_dihedral_angle_1_deg	6.562
r_scangle_it	3.541
r_scbond_it	2.263
r_mcangle_it	1.717
r_angle_refined_deg	1.524
r_mcbond_it	0.984
r_nbtor_refined	0.311
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.169
r_xyhbond_nbd_refined	0.138
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.116
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3169
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection