5DDI | pdb_00005ddi

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle - holo enzyme - at 2.40 Angstrom resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	54.7% w/v ammonium sulfate, 0.05 M HEPES, 0.005 M EDTA, 0.005 M 1,10-orthophenanthroline

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.9	α = 90
b = 138.97	β = 90
c = 222.3	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	IMAGE PLATE	MARRESEARCH		1995-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.0	EMBL/DESY, HAMBURG	BW7A

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	2.4	25	99.3	0.049	16.8	7.1	54851	54851		1

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	2.4	2.45	98.8		0.11		4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.4	23.98	53174	1699	99.14	0.2494	0.248	0.2523	0.2946	0.2987	RANDOM	36.604

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]
-0.14			0.08		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.696
r_dihedral_angle_4_deg	19.302
r_dihedral_angle_3_deg	16.787
r_dihedral_angle_1_deg	5.934
r_angle_refined_deg	1.72
r_angle_other_deg	1.254
r_mcangle_it	0.806
r_mcbond_it	0.455
r_mcbond_other	0.455
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7533
Nucleic Acid Atoms
Solvent Atoms	383
Heterogen Atoms	162

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing