2V19 | pdb_00002v19

Crystal structure of the T. thermophilus dodecin R45A mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MOG	PDB ENTRY 1MOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M AMMONIUM SULFATE, 0.05 M SODIUM CACODYLATE, PH 6.5 AND 15% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.7	57.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.294	α = 90
b = 68.494	β = 90
c = 229.891	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	11	IMAGE PLATE	MARRESEARCH	OSMIC MIRRORS	2005-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591

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	2.58	25	95.9	0.09	13.2	3.7		32742

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	2.59	2.66			0.24	3.5

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 1MOG	2.59	25	31678	1018	96.1	0.207	0.206	0.23	0.234	0.25	RANDOM	30.33

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]
2.85			-1.6		-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.487
r_dihedral_angle_3_deg	17.381
r_dihedral_angle_4_deg	15.232
r_dihedral_angle_1_deg	10.928
r_scangle_it	4.544
r_scbond_it	3.049
r_mcangle_it	1.86
r_mcbond_it	1.528
r_angle_refined_deg	1.002
r_angle_other_deg	0.572
r_symmetry_vdw_other	0.396
r_symmetry_vdw_refined	0.255
r_nbd_other	0.228
r_nbd_refined	0.22
r_nbtor_refined	0.193
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.156
r_nbtor_other	0.087
r_chiral_restr	0.062
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6336
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	891

Software

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