3MTA | pdb_00003mta

Glycogen phosphorylase complexed with 3-bromobenzaldehyde-4-(beta-D-glucopyranosyl)-thiosemicarbazone

X-RAY DIFFRACTION

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	Crystals grown from 20 mg/ml protein in a buffer of 10 mM BES, pH 6.7, 1mM EDTA, 3mM DTT. Crystals soaked with 10mM inhibitor in 20% DMSO soaked for 21 hrs, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.916	α = 90
b = 128.916	β = 90
c = 116.782	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		2008-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.97976	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	2.23	30	98.1	0.071	9.67	3.6	47672	47672		-3	36.5

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)
	2.23	2.27	96.6		0.462	3.55	3.7	2290

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	2.23	30	45222	45222	2413	98.19	0.19763	0.19575	0.2	0.23282	0.23	RANDOM	42.343

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]
0.08			0.08		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.701
r_dihedral_angle_4_deg	19.58
r_dihedral_angle_3_deg	16.03
r_dihedral_angle_1_deg	5.264
r_scangle_it	2.204
r_scbond_it	1.371
r_angle_refined_deg	1.099
r_mcangle_it	1.08
r_mcbond_it	0.619
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.701
r_dihedral_angle_4_deg	19.58
r_dihedral_angle_3_deg	16.03
r_dihedral_angle_1_deg	5.264
r_scangle_it	2.204
r_scbond_it	1.371
r_angle_refined_deg	1.099
r_mcangle_it	1.08
r_mcbond_it	0.619
r_nbtor_refined	0.305
r_nbd_refined	0.189
r_symmetry_vdw_refined	0.18
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6604
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	48

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.