2FCL | pdb_00002fcl

Crystal structure of a putative nucleotidyltransferase (tm1012) from Thermotoga maritima at 1.35 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EWR	pdb entry 2ewr

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	5.6	277	15.0% Glycerol, 0.17M NH4OAc, 25.5% PEG-4000, 0.1M Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.769	α = 73.69
b = 36.382	β = 85.51
c = 39.785	γ = 78.97

Symmetry
Space Group	P 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 315	Flat mirror (vertical focusing)	2005-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979454	SSRL	BL11-1

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	1.2	25.88	73.5	0.034	0.034	20.3	2.3		39827			11.7

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	1.23	17.6		0.146	0.146	5.7	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 2ewr	1.2	24.28	37613	2028	74.77	0.142	0.14	0.15	0.17	0.18	RANDOM	13.634

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]
-0.77	0.31	-0.17	-0.24	0.22	0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.504
r_dihedral_angle_4_deg	12.17
r_dihedral_angle_3_deg	10.994
r_dihedral_angle_1_deg	5.901
r_scangle_it	4.992
r_sphericity_bonded	4.336
r_scbond_it	3.749
r_mcangle_it	2.872
r_mcbond_it	2.188
r_rigid_bond_restr	2.002
r_mcbond_other	1.445
r_angle_refined_deg	1.335
r_angle_other_deg	0.785
r_symmetry_vdw_other	0.257
r_nbd_refined	0.237
r_xyhbond_nbd_refined	0.207
r_nbd_other	0.189
r_nbtor_refined	0.183
r_symmetry_hbond_refined	0.141
r_chiral_restr	0.082
r_nbtor_other	0.082
r_symmetry_vdw_refined	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1308
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	14

Software

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