2G80 | pdb_00002g80

Crystal structure of UTR4 protein (Unknown transcript 4 protein) (yel038w) from Saccharomyces cerevisiae at 2.28 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZS9	pdb entry 1zs9A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP		290	21.00% PEG 3350, 0.10M NP_Magnesium Nitrate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.688	α = 90
b = 102.016	β = 92.68
c = 77.227	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 210		2004-09-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.28	61.54	99.9	0.088	0.088	4.5	3.6		52775			42.6

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	2.28	2.4	99.9		0.359	0.359	1.7	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	pdb entry 1zs9A	2.28	61.53	52503	2673	99.87	0.18	0.177	0.18	0.229	0.23	RANDOM	37.416

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]
1.67		-1	-1.76		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.321
r_dihedral_angle_4_deg	14.678
r_dihedral_angle_3_deg	9.746
r_scangle_it	6.423
r_scbond_it	4.84
r_dihedral_angle_1_deg	3.801
r_mcangle_it	2.754
r_mcbond_it	1.826
r_angle_refined_deg	1.604
r_angle_other_deg	1.196
r_mcbond_other	0.427
r_nbd_refined	0.173
r_nbtor_refined	0.155
r_symmetry_vdw_refined	0.142
r_symmetry_vdw_other	0.138
r_symmetry_hbond_refined	0.136
r_nbd_other	0.122
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.105
r_nbtor_other	0.071
r_metal_ion_refined	0.025
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6888
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing