4MVJ | pdb_00004mvj

2.85 Angstrom Resolution Crystal Structure of Glyceraldehyde 3-phosphate Dehydrogenase A (gapA) from Escherichia coli Modified by Acetyl Phosphate.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S7C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein - 7.3mg/mL, 0.15M Sodium chloride, 0.01M Tris-HCl pH 8.3, Screen - PACT (G2), 0.2 M Sodium bromide, 0.1 M Bis Tris propane pH 7.5, 20 % (w/v) PEG 3350, 10mM ACP., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.879	α = 90
b = 69.688	β = 98.8
c = 271.923	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD	Beryllium lenses	2013-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.85	30	100	0.086	15.5	3.8	127301	127301		-3	75.3

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	2.85	2.9	100		0.637	2	3.8	6384

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	1S7C	2.85	29.91	120750	120750	6389	99.8	0.18774	0.18774	0.18582	0.18	0.2235	0.22	RANDOM	74.416

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]
-1.56		-1.03	1.44		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.67
r_dihedral_angle_4_deg	17.904
r_long_range_B_refined	9.968
r_long_range_B_other	9.952
r_dihedral_angle_3_deg	9.892
r_scangle_other	7.667
r_mcangle_it	5.884
r_mcangle_other	5.884
r_scbond_it	5.412
r_scbond_other	5.365
r_mcbond_it	3.92
r_mcbond_other	3.919
r_dihedral_angle_1_deg	2.17
r_angle_refined_deg	1.904
r_angle_other_deg	1.315
r_chiral_restr	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.011
r_bond_other_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	39992
Nucleic Acid Atoms
Solvent Atoms	443
Heterogen Atoms	540

Software

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