1VPQ | pdb_00001vpq

CRYSTAL STRUCTURE OF a DUF72 family protein (TM1631) FROM THERMOTOGA MARITIMA MSB8 AT 2.20 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	9.5	277	1.26M (NH4)2SO4, 0.2M NaCl 0.1M CHES pH9.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP	8.3	277	0.2M K3Citrate, 20.0% PEG-3350, No Buffer pH 8.3, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02
2.28	45.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.286	α = 90
b = 136.238	β = 90
c = 80.461	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315	flat mirror	2002-02-07	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	APS	Rosenbaum-Rock vertical focusing mirror	2003-11-15	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1
2	SYNCHROTRON	APS BEAMLINE 19-BM	0.98036, 0.98014, 0.96427	APS	19-BM

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	2.2	49.63	88.4	0.095	10.5	3.2		13378			37.6

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	2.2	2.26	67.3		0.4	2.8	2.2	736

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD + MOLECULAR REPLACEMENT	THROUGHOUT	2.2	49.63	12722	656	87.61	0.20872	0.20602	0.21	0.26256	0.27	RANDOM	29.804

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			-2.85		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.379
r_dihedral_angle_4_deg	19.712
r_dihedral_angle_3_deg	14.154
r_dihedral_angle_1_deg	5.854
r_scangle_it	1.302
r_angle_refined_deg	1.05
r_scbond_it	0.896
r_angle_other_deg	0.739
r_mcangle_it	0.604
r_mcbond_it	0.526
r_symmetry_hbond_refined	0.303
r_nbd_refined	0.189
r_nbtor_refined	0.189
r_nbd_other	0.186
r_xyhbond_nbd_refined	0.173
r_symmetry_vdw_other	0.173
r_symmetry_vdw_refined	0.152
r_nbtor_other	0.082
r_chiral_restr	0.06
r_mcbond_other	0.054
r_bond_refined_d	0.008
r_bond_other_d	0.005
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2180
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	15

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling