3GCM | pdb_00003gcm

Crystal Structure of E. coli polynucleotide phosphorylase bound to RNA and RNase E

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E3H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293.15	0.2 M ammonium hydrogen citrate, 17 % w/v PEG 3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 176.335	α = 90
b = 176.335	β = 90
c = 189.628	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	120	CCD	MARMOSAIC 225 mm CCD	Monochromator	2006-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	20	99.3		6.6	102846	97645	2	2	27.176

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)
	2.5	2.59	99.5		0.619	2.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	1E3H	2.5	20	102846	97645	5134	99.36	0.201	0.16911	0.16639	0.2	0.22065	0.23	RANDOM	27.176

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.495
r_dihedral_angle_4_deg	20.703
r_dihedral_angle_3_deg	15.951
r_dihedral_angle_1_deg	6.735
r_scangle_it	5.44
r_scbond_it	3.361
r_mcangle_it	2.01
r_angle_refined_deg	1.939
r_angle_other_deg	1.247
r_mcbond_it	1.229
r_nbtor_refined	0.309
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.193
r_xyhbond_nbd_refined	0.161
r_symmetry_hbond_refined	0.159
r_chiral_restr	0.152
r_nbd_other	0.14
r_nbtor_other	0.051
r_bond_refined_d	0.022
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_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	12865
Nucleic Acid Atoms
Solvent Atoms	884
Heterogen Atoms	167

Software

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