3F9R | pdb_00003f9r

Crystal Structure of Trypanosoma Brucei phosphomannosemutase, TB.10.700.370

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	2.0 M (NH4)2SO4, 0.2 M NaCl, 0.1 M NaCacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.927	α = 90
b = 46.994	β = 90
c = 94.494	γ = 90

Symmetry
Space Group	P 21 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	IMAGE PLATE	RIGAKU RAXIS IV++		2008-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5408

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	1.8	50	99.9	0.122	0.115	17.834	6.2	44920	44877			29.343

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)
	1.8	1.86	99.3		0.862	0.638	1.4	4.4	4370

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.85	50	41076	2074	99.89	0.202	0.199	0.23	0.266	0.28	RANDOM	31.63

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]
-0.04			1.03		-0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.764
r_dihedral_angle_4_deg	17.14
r_dihedral_angle_3_deg	14.517
r_dihedral_angle_1_deg	6.119
r_scangle_it	3.215
r_scbond_it	2.203
r_angle_refined_deg	1.471
r_mcangle_it	1.204
r_mcbond_it	0.802
r_nbtor_refined	0.307
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.197
r_symmetry_hbond_refined	0.168
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3931
Nucleic Acid Atoms
Solvent Atoms	378
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction