1SZJ | pdb_00001szj

STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM PALINURUS VERSICOLOR REFINED 2.0 ANGSTROM RESOLUTION

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		HOMARUS AMERICANUS HOLO-GAPDH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.1	280	THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULPHATE IN 0.1M PHOSPHATE BUFFER (PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULPHATE IN SAME BUFFER. THE CRYSTALLIZATION WAS CARRIED OUT AT 280K.

Crystal Properties
Matthews coefficient	Solvent content
3.27	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.4	α = 90
b = 99.9	β = 114.48
c = 80.79	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	280	DIFFRACTOMETER	WEISSENBERG		1994-05-17	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A		Photon Factory	BL-6A

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	1.7	100	83.5	0.069	3.9	1.4		84900			21.93

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	1.7	1.74	56.5		0.069	1.6	1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	HOMARUS AMERICANUS HOLO-GAPDH	2	6	3	49184	5073	81.64	0.168	0.168	0.16	0.223	RANDOM	32.39

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	25.92
x_angle_deg	2.85
x_improper_angle_d	1.35
x_bond_d	0.014
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5012
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	108

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
WEIS	data reduction
CCP4	data scaling
X-PLOR	phasing