3RM5 | pdb_00003rm5

Structure of Trifunctional THI20 from Yeast

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YAF	PDB entries 1YAF, 1JXH
experimental model	PDB	1JXH	PDB entries 1YAF, 1JXH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	10-14% Peg 8K, 0.2 M Calcium Acetate, 0.1 M Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.704	α = 90
b = 140.096	β = 90
c = 143.273	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2009-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.979	APS	24-ID-C

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	2.68	100.17	92.8	0.094	7.1	2.8		31670

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	2.68	2.8	70		0.329		1.5	2348

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 entries 1YAF, 1JXH	2.68	50	31625	1606	91.45	0.2398	0.2377	0.2326	0.2786	0.2743	RANDOM	55.3917

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]
-0.25			-1.36		1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.736
r_dihedral_angle_3_deg	17.051
r_dihedral_angle_4_deg	14.81
r_dihedral_angle_1_deg	4.36
r_angle_refined_deg	0.912
r_scangle_it	0.741
r_mcangle_it	0.441
r_scbond_it	0.422
r_mcbond_it	0.238
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7794
Nucleic Acid Atoms
Solvent Atoms	57
Heterogen Atoms	15

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection