3BCU | pdb_00003bcu

Glucogen Phosphorylase complex with thymidine

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	10mM Bes buffer, 3mM DDT, pH6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.626	α = 90
b = 128.626	β = 90
c = 116.47	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	298	CCD	MAR CCD 165 mm		2005-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.81	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.03	30	98.8	0.047	17.6	6.6	62744	62744		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.03	2.06	98.5		0.442	3.8	6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2PRJ	2.03	21.59	59516	3179	98.8	0.19094	0.19032	0.1898	0.20227	0.2029	RANDOM	36.449

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]
0.91			0.91		-1.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.225
r_dihedral_angle_4_deg	17.813
r_dihedral_angle_3_deg	15.187
r_dihedral_angle_1_deg	5.035
r_scangle_it	2.012
r_scbond_it	1.234
r_angle_refined_deg	1.025
r_mcangle_it	0.961
r_mcbond_it	0.561
r_nbtor_refined	0.302
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.148
r_xyhbond_nbd_refined	0.105
r_symmetry_hbond_refined	0.091
r_chiral_restr	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6638
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling