1YDV | pdb_00001ydv

TRIOSEPHOSPHATE ISOMERASE (TIM)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5TIM	TRYPANOSOMAL TIM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		10 MG/ML PROTEIN IN 12% PEG 6000 IN HEPES BUFFER PH 7.5, 1MM DTT EQUILIBRATED AGAINST 24% PEG 6000 IN HEPES BUFFER PH 7.5, 1MM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.55	48.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.91	α = 90
b = 47.64	β = 108.26
c = 118.43	γ = 90

Symmetry
Space Group	C 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	300	IMAGE PLATE	MARRESEARCH	FRANCS		M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

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	15	92	0.089		4		25936		2	19.6

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)
	2.2	2.3	83.9		0.252

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	TRYPANOSOMAL TIM	2.2	10	2	24508	2497	92	0.198	0.198	0.19	0.255	RANDOM	14

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	23.6
x_scangle_it	6.6
x_scbond_it	4.48
x_mcangle_it	3.36
x_mcbond_it	2.35
x_angle_deg	1.4
x_improper_angle_d	1.28
x_bond_d	0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3914
Nucleic Acid Atoms
Solvent Atoms	171
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing