7C5P

Crystal Structure Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with G3P at 2.35 Angstrom resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7C5F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	293	100mM sodium PBS pH 6.1, 16%(w/v) PEG 1000, 200mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.339	α = 90
b = 90.339	β = 90
c = 341.547	γ = 90

Symmetry
Space Group	P 41 21 2

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	ADSC QUANTUM 315r		2016-09-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97776	SSRF	BL18U1

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	2.35	50.01	100	0.19	14	11.3		60156

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	2.35	2.39	100		0.624	3.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7C5F	2.35	50	56884	3003	99.46	0.15778	0.15497	0.20975	RANDOM	32.346

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]
1.08			1.08		-2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.169
r_dihedral_angle_4_deg	20.005
r_dihedral_angle_3_deg	13.678
r_dihedral_angle_1_deg	7.227
r_long_range_B_refined	6.034
r_long_range_B_other	6.033
r_scangle_other	4.474
r_mcangle_other	3.343
r_mcangle_it	3.341
r_scbond_it	3.046
r_scbond_other	3.041
r_mcbond_it	2.245
r_mcbond_other	2.238
r_angle_refined_deg	1.793
r_angle_other_deg	1.012
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10083
Nucleic Acid Atoms
Solvent Atoms	615
Heterogen Atoms	246

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing