2VOM | pdb_00002vom

Structural basis of human triosephosphate isomerase deficiency. Mutation E104D and correlation to solvent perturbation.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		100 MM TRIS PH 8.5, 20% PEG MME2000, 4% POLYPROPYLENE GLYCOL P400, 10 MM NICL2

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 320.521	α = 90
b = 47.288	β = 97.2
c = 68.957	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	113	CCD	MARRESEARCH	HIGH-RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR	2007-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-ID

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	1.85	60.2	93	0.13	0.11	9.6	3.4		81960		2	18.9

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	1.85	1.95	93		0.39	0.32	3.3	3.57

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	PDB ENTRY 1WYI	1.85	50	81958	4142	92.8	0.2194	0.2194	0.22	0.2525	0.23	RANDOM	23.21

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]
1.265		0.146	0.45		-1.715

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.58
c_angle_deg	1.25063
c_improper_angle_d	0.71
c_bond_d	0.004809
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7372
Nucleic Acid Atoms
Solvent Atoms	611
Heterogen Atoms

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing