3MT9 | pdb_00003mt9

Glycogen phosphorylase complexed with 4-nitrobenzaldehyde-4-(beta-D-glucopyranosyl)-thiosemicarbazone

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	SMALL TUBES	6.7	289	20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA and 3 mM DTT. Crystals soaked with 6.7mM inhibitor in 20% DMSO for 3 hrs, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.27	α = 90
b = 128.27	β = 90
c = 115.779	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	CCD	MARMOSAIC 225 mm CCD		2007-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.04498	SRS	PX10.1

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	2.05	35.7	99.7	0.093	19.5	6.4	60721	60721		-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)
	2.05	2.16	100		0.45	5.6	6.3

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2PRJ	2.05	35.69	57608	57607	3081	99.51	0.17503	0.17344	0.1734	0.20498	0.2045	RANDOM	28.436

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]
0.05			0.05		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.749
r_dihedral_angle_4_deg	20.823
r_dihedral_angle_3_deg	15.713
r_dihedral_angle_1_deg	5.424
r_scangle_it	3.154
r_scbond_it	1.838
r_mcangle_it	1.224
r_angle_refined_deg	1.147
r_mcbond_it	0.628
r_nbtor_refined	0.305
r_nbd_refined	0.183
r_symmetry_vdw_refined	0.151
r_symmetry_hbond_refined	0.122
r_xyhbond_nbd_refined	0.097
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6604
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing