3FYC | pdb_00003fyc

Crystal Structure of Dim1 from the thermophilic archeon, Methanocaldococcus jannaschi

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QYR	composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9
experimental model	PDB	2H1R	composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9
experimental model	PDB	1ZQ9	composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	PEG 3350 (18%), 25 mM MES, 50 mM Na2HPO4, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.384	α = 90
b = 72.274	β = 91.87
c = 95.883	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	IMAGE PLATE	RIGAKU RAXIS IV++	Rigaku Varimax confocal optics	2008-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.15	32.77	94.9	0.091	12.4	6.62	30159	28619			37.9

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)
	2.15	2.23	91.9		0.361	4.7	6.65	3014

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	composite model consisting of monomers from pdb entries 1QYR, 2H1R and 1ZQ9	2.15	32	25730	2873	94.89	0.20946	0.20237	0.2101	0.27332	RANDOM	36.407

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]
-2.26		-1.33	3.05		-0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.084
r_dihedral_angle_4_deg	20.115
r_dihedral_angle_3_deg	15.153
r_dihedral_angle_1_deg	5.622
r_scangle_it	4.135
r_scbond_it	2.692
r_mcangle_it	1.68
r_angle_refined_deg	1.123
r_mcbond_it	0.823
r_nbtor_refined	0.3
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.167
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.081
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4307
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	50

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling