3G4C | pdb_00003g4c

Flavine dependant thymidylate syntahse S88C mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O26	Native structure with dUMP (PDB code: 1O26)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	40% PEG 200, 0.1M Tris-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.897	α = 90
b = 116.495	β = 90
c = 140.986	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	MARMOSAIC 325 mm CCD	Flat collimating mirror, double crystal monochromator, toroid focusing mirror	2007-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9795	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.05	46.22	99.9	0.074	12	4.2	56600	56600

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	2.05	2.1	100		0.999	0.63	2.1	4.3	4137

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	Difference fourier	THROUGHOUT	Native structure with dUMP (PDB code: 1O26)	2.05	46.22	53694	2843	99.91	0.20248	0.19983	0.2	0.25358	0.25	RANDOM	25.267

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]
3.77			-1.38		-2.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.375
r_dihedral_angle_4_deg	16.867
r_dihedral_angle_3_deg	14.801
r_dihedral_angle_1_deg	6.228
r_scangle_it	2.519
r_scbond_it	1.689
r_angle_refined_deg	1.609
r_mcangle_it	1.171
r_angle_other_deg	0.965
r_mcbond_it	0.745
r_symmetry_vdw_other	0.253
r_nbd_other	0.208
r_nbd_refined	0.202
r_mcbond_other	0.202
r_symmetry_vdw_refined	0.199
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.157
r_symmetry_hbond_refined	0.1
r_nbtor_other	0.091
r_chiral_restr	0.09
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6950
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	292

Software

Software
Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing