1VPV

Crystal structure of a degv lipid binding protein (tm1468) from thermotoga maritima at 2.45 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6.5	293	0.1M Cacodylate pH 6.5, 0.2M Mg(oAc)2, 27.5% PEG-8000, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.42	48.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.256	α = 90
b = 103.256	β = 90
c = 115.863	γ = 90

Symmetry
Space Group	P 41 21 2

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	APS	sagitally focusing. 2nd crystal, Rosenbaum-Rock vertical focusing mirror	2003-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	2.453	50	96.36	0.098	13.77	4.09		22755			43.04

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.453	2.55	97.78		0.293	4.88	3.89	2244

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	1mgp	2.45	47.16	21579	1174	96.28	0.18355	0.17987	0.19	0.25188	0.25	RANDOM	24.207

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]
0.27			0.27		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.628
r_dihedral_angle_4_deg	17.625
r_dihedral_angle_3_deg	15.947
r_scangle_it	8.135
r_dihedral_angle_1_deg	6.044
r_scbond_it	5.82
r_mcangle_it	2.856
r_mcbond_it	2.262
r_angle_refined_deg	1.549
r_angle_other_deg	0.845
r_mcbond_other	0.584
r_nbd_refined	0.213
r_symmetry_vdw_other	0.193
r_nbd_other	0.19
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.155
r_symmetry_vdw_refined	0.139
r_chiral_restr	0.089
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4400
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	46

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement