6T4R | pdb_00006t4r

Crystal structure of Trypanosoma brucei Morn1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6T4D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295.15	0.166 M Tris-HCl pH 8.8, 0.15 M MgCl2, 0.45 M KI, 24% PEG 2000 MME, and 4% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.039	α = 90
b = 27.63	β = 101.833
c = 114.542	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2013-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.979	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.35	48.28	95.4	0.092	0.1	0.04	0.998	13.4	6.1		17460			18.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	71.5		0.466	0.532	0.25	0.897	2.8	4.1

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6T4D	2.352	48.28	17452	818	95.231	0.223	0.2209	0.23	0.259	0.27	35.095

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]
-1.493		-4.491	-1.163		4.171

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.529
r_dihedral_angle_3_deg	16.164
r_dihedral_angle_4_deg	16.071
r_lrange_it	7.396
r_lrange_other	7.385
r_dihedral_angle_1_deg	7.352
r_scangle_it	5.573
r_scangle_other	5.573
r_mcangle_other	4.449
r_mcangle_it	4.446
r_scbond_it	3.596
r_scbond_other	3.596
r_mcbond_it	2.881
r_mcbond_other	2.867
r_angle_other_deg	2.435
r_angle_refined_deg	1.258
r_symmetry_xyhbond_nbd_other	0.282
r_symmetry_nbd_refined	0.219
r_nbd_other	0.214
r_symmetry_nbd_other	0.201
r_nbd_refined	0.182
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.089
r_symmetry_nbtor_other	0.067
r_chiral_restr	0.044
r_bond_other_d	0.037
r_gen_planes_other	0.006
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3404
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing