2FYX | pdb_00002fyx

Crystal structure of a putative transposase (dr_0177) from deinococcus radiodurans r1 at 1.90 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F4F	2f4f chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	277	2.0M (NH4)2SO4, 0.2M NaCl, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.787	α = 90
b = 66.787	β = 90
c = 81.18	γ = 120

Symmetry
Space Group	P 32

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 4		2004-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3		ALS	5.0.3

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	1.9	28.915	100	0.045	0.045	9.9	3.9		31895

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	1.9	1.95		100	0.547	0.547	1.3	2.9

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 (All)	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	2f4f chain A	1.9	27.24	31862	1608	99.87	0.162	0.16159	0.16	0.17	0.191	0.2	RANDOM	40.291

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]
0.43	0.21		0.43		-0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.224
r_dihedral_angle_4_deg	20.437
r_dihedral_angle_3_deg	13.763
r_scangle_it	7.198
r_dihedral_angle_1_deg	6.243
r_scbond_it	5.748
r_mcangle_it	3.378
r_mcbond_it	2.466
r_angle_refined_deg	1.703
r_angle_other_deg	0.87
r_mcbond_other	0.609
r_symmetry_vdw_other	0.273
r_nbd_refined	0.21
r_nbtor_refined	0.186
r_symmetry_hbond_refined	0.184
r_nbd_other	0.174
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.113
r_symmetry_vdw_refined	0.09
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.018
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2046
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	48

Software

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