3KZV

The crystal structure of a cytoplasmic protein with unknown function from Saccharomyces cerevisiae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	289	0.1M Bis-tris, 5% Iso-propanol, 2.4M NH4SO4,1/1600 chymotrypsin, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.413	α = 90
b = 117.413	β = 90
c = 89.488	γ = 90

Symmetry
Space Group	I 41 2 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	ADSC QUANTUM 315r	mirrors	2008-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-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	2	83.05	98.69	0.148	1.5	16.3	20314	20048	2	1.5

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	2	2.052	93.58		0.536	36.9	16.3	1558

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2	83.05	20314	20048	1080	98.69	0.19409	0.19133	0.24461	RANDOM	35.676

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]
0.52			0.52		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.454
r_dihedral_angle_4_deg	20.96
r_dihedral_angle_3_deg	17.512
r_dihedral_angle_1_deg	7.839
r_scangle_it	6.173
r_scbond_it	3.891
r_mcangle_it	2.423
r_angle_refined_deg	2.284
r_mcbond_it	1.368
r_chiral_restr	0.159

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.454
r_dihedral_angle_4_deg	20.96
r_dihedral_angle_3_deg	17.512
r_dihedral_angle_1_deg	7.839
r_scangle_it	6.173
r_scbond_it	3.891
r_mcangle_it	2.423
r_angle_refined_deg	2.284
r_mcbond_it	1.368
r_chiral_restr	0.159
r_bond_refined_d	0.024
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1885
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	18

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.