4GNJ | pdb_00004gnj

Crystal Structure Analysis of Leishmania siamensis Triosephosphate Isomerase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	291	0.20M calcium acetate, 0.10M sodium cacodylate trihydrate, 18% PEG 8000, pH 6.5, MICROBATCH, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.58	α = 90
b = 78.79	β = 101.15
c = 83.16	γ = 90

Symmetry
Space Group	P 1 2 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	CCD	RAYONIX SX-165mm	HELIOS	2011-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	1.93	81.6	93.7	0.054	0.202	14.2	3.3		35257	2	2	16.4

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	1.93	2.03	90.2		0.202	0.202	3.8	3.1	15450

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	PDB ENTRY 1AMK	1.93	21.61	2	2	33449	1793	93.23	0.15373	0.15373	0.15132	0.1458	0.19932	0.1912	RANDOM	15.209

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]
0.1		0.29	0.52		-0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.698
r_dihedral_angle_4_deg	17.724
r_dihedral_angle_3_deg	12.958
r_dihedral_angle_1_deg	6.083
r_scangle_it	3.021
r_scbond_it	1.837
r_angle_refined_deg	1.358
r_mcangle_it	0.982
r_mcbond_it	0.56
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3749
Nucleic Acid Atoms
Solvent Atoms	365
Heterogen Atoms	3

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling