2SKC | pdb_00002skc

PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH FLUOROPHOSPHATE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PRJ	PDB ENTRY 2PRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	289	T-STATE PYRIDOXAL PHOSPHORYLASE B, FROM RABBIT MUSCLE, WAS CO-CRYSTALLIZED WITH 8-10 MM FLUOROPHOSPHATE IN A MEDIUM CONSISTING OF 15-25 MG/ML ENZYME, 2 MM IMP, 2 MM SPERMINE, 50 MM GLUCOSE, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (16 DEGREE C). JUST BEFORE DATA COLLECTION, THE CRYSTALS WERE TRANSFERRED TO A FRESH BUFFER SOLUTION, CONTAINING THE SAME CONSTITUENTS AS THEIR MOTHER LIQUOR WITH THE EXCEPTION OF THE PROTEIN., VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.47	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.5	α = 90
b = 128.5	β = 90
c = 116.3	γ = 90

Symmetry
Space Group	P 43 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	293	FILM			1993-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX7.2		SRS	PX7.2

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	27.84	84.55	0.077		3.4		32599

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.51	52.1

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PRJ	2.4	27.84	32599	32599		84.55	0.167	0.167	0.217	RANDOM

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	25.5
x_angle_deg	1.4
x_improper_angle_d	0.72
x_bond_d	0.008
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	6749
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	51

Software

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