4MVA | pdb_00004mva

1.43 Angstrom Resolution Crystal Structure of Triosephosphate Isomerase (tpiA) from Escherichia coli in Complex with Acetyl Phosphate.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 7.4mg/mL, 0.15M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (F11), 0.2M Sodium chloride, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 10mM ACP, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.535	α = 90
b = 67.529	β = 90
c = 150.336	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 300 mm CCD	Beryllium lenses	2013-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.43	30	99.9	0.062	22.7	6.1	88659	88659		-3	16.2

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)
1	1.43	1.45	100		0.534	3.4	6	4416

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 1TRE	1.43	29.24	83946	83946	4433	99.91	0.13567	0.13567	0.13456	0.14	0.15614	0.16	RANDOM	19.023

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]
-0.09			0.66		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.623
r_dihedral_angle_4_deg	10.242
r_dihedral_angle_3_deg	9.701
r_long_range_B_refined	6.988
r_long_range_B_other	6.384
r_dihedral_angle_1_deg	3.588
r_scangle_other	3.129
r_scbond_it	2.084
r_scbond_other	2.084
r_mcangle_other	2.044
r_mcangle_it	2.043
r_angle_refined_deg	1.471
r_mcbond_it	1.261
r_mcbond_other	1.258
r_angle_other_deg	0.762
r_chiral_restr	0.083
r_gen_planes_refined	0.017
r_gen_planes_other	0.016
r_bond_refined_d	0.01
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3780
Nucleic Acid Atoms
Solvent Atoms	837
Heterogen Atoms	37

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling