2QN1 | pdb_00002qn1

Glycogen Phosphorylase b in complex with asiatic acid

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	10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.72	α = 90
b = 128.72	β = 90
c = 116.638	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	MAR CCD 165 mm		2007-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8088	EMBL/DESY, HAMBURG	X13

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	2.4	90.91	100	0.07	15.5	5.3	38832	38832		-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)
	2.4	2.44	99.9		0.471	4.2	5.4

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 (All)	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	2.401	90.91	36836	36836	1942	99.88	0.18067	0.18067	0.17922	0.18	0.20752	0.21	RANDOM	40.268

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]
1.02			1.02		-2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.175
r_dihedral_angle_4_deg	19.654
r_dihedral_angle_3_deg	16.113
r_dihedral_angle_1_deg	5.393
r_scangle_it	2.179
r_scbond_it	1.299
r_angle_refined_deg	1.129
r_mcangle_it	1.059
r_mcbond_it	0.601
r_nbtor_refined	0.305
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.165
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.081
r_symmetry_hbond_refined	0.063
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6638
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	35

Software

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