3GME | pdb_00003gme

Crystal Structure of Polynucleotide Phosphorylase in complex with RNase E and manganese

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION			2.5 M NaCl, 9 % w/v PEG 6000, 20 mM Na- citrate, 20 mM manganese acetate , VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.574	α = 90
b = 158.574	β = 90
c = 156.118	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2008-08-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	1.07	Diamond	I02

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	25.91	96.7	0.125		2.9	27941	27938	2	2

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)
	2.4	2.48	96.7		0.432	1.8	2.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MOLECULAR REPLACEMENT	THROUGHOUT	2.4	25.91	27941	27938	1490	99.34	0.28621	0.28561	0.28	0.29758	0.29	RANDOM	50.586

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]
-0.01	-0.01		-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.144
r_dihedral_angle_3_deg	12.752
r_dihedral_angle_4_deg	12.138
r_scangle_it	5.98
r_scbond_it	3.819
r_dihedral_angle_1_deg	3.575
r_mcangle_it	2.7
r_mcbond_it	1.533
r_angle_refined_deg	0.765
r_nbtor_refined	0.284
r_nbd_refined	0.136
r_symmetry_vdw_refined	0.118
r_symmetry_hbond_refined	0.106
r_xyhbond_nbd_refined	0.096
r_chiral_restr	0.045
r_bond_refined_d	0.005
r_gen_planes_refined	0.001
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	3694
Nucleic Acid Atoms
Solvent Atoms	158
Heterogen Atoms	2

Software

Software
Software Name	Purpose
HKL-3000	data collection
REFMAC	refinement